fix(ingestion): align CALLS edge sourceId with node ID format

findEnclosingFunctionId generated IDs without :startLine suffix,
but node creation includes it. This caused every CALLS edge to
reference a non-existent source node, making the process detector
find 0 entry points and produce 0 execution flows.

Bumps to 1.3.9.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.claude/skills/gitnexus/gitnexus-cli/SKILL.md

@@ -22,7 +22,7 @@ Run from the project root. This parses all source files, builds the knowledge gr
 | `--force`      | Force full re-index even if up to date                           |
 | `--embeddings` | Enable embedding generation for semantic search (off by default) |
 
-**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale. In Claude Code, a PostToolUse hook runs `analyze` automatically after `git commit` and `git merge`, preserving embeddings if previously generated.
+**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale.
 
 ### status — Check index freshness
 

.claude/skills/gitnexus/gitnexus-debugging/SKILL.md

@@ -1,89 +1,89 @@
----
-name: gitnexus-debugging
-description: "Use when the user is debugging a bug, tracing an error, or asking why something fails. Examples: \"Why is X failing?\", \"Where does this error come from?\", \"Trace this bug\""
----
-
-# Debugging with GitNexus
-
-## When to Use
-
-- "Why is this function failing?"
-- "Trace where this error comes from"
-- "Who calls this method?"
-- "This endpoint returns 500"
-- Investigating bugs, errors, or unexpected behavior
-
-## Workflow
-
-```
-1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
-2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
-3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
-4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
-```
-
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
-
-## Checklist
-
-```
-- [ ] Understand the symptom (error message, unexpected behavior)
-- [ ] gitnexus_query for error text or related code
-- [ ] Identify the suspect function from returned processes
-- [ ] gitnexus_context to see callers and callees
-- [ ] Trace execution flow via process resource if applicable
-- [ ] gitnexus_cypher for custom call chain traces if needed
-- [ ] Read source files to confirm root cause
-```
-
-## Debugging Patterns
-
-| Symptom              | GitNexus Approach                                          |
-| -------------------- | ---------------------------------------------------------- |
-| Error message        | `gitnexus_query` for error text → `context` on throw sites |
-| Wrong return value   | `context` on the function → trace callees for data flow    |
-| Intermittent failure | `context` → look for external calls, async deps            |
-| Performance issue    | `context` → find symbols with many callers (hot paths)     |
-| Recent regression    | `detect_changes` to see what your changes affect           |
-
-## Tools
-
-**gitnexus_query** — find code related to error:
-
-```
-gitnexus_query({query: "payment validation error"})
-→ Processes: CheckoutFlow, ErrorHandling
-→ Symbols: validatePayment, handlePaymentError, PaymentException
-```
-
-**gitnexus_context** — full context for a suspect:
-
-```
-gitnexus_context({name: "validatePayment"})
-→ Incoming calls: processCheckout, webhookHandler
-→ Outgoing calls: verifyCard, fetchRates (external API!)
-→ Processes: CheckoutFlow (step 3/7)
-```
-
-**gitnexus_cypher** — custom call chain traces:
-
-```cypher
-MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
-RETURN [n IN nodes(path) | n.name] AS chain
-```
-
-## Example: "Payment endpoint returns 500 intermittently"
-
-```
-1. gitnexus_query({query: "payment error handling"})
-   → Processes: CheckoutFlow, ErrorHandling
-   → Symbols: validatePayment, handlePaymentError
-
-2. gitnexus_context({name: "validatePayment"})
-   → Outgoing calls: verifyCard, fetchRates (external API!)
-
-3. READ gitnexus://repo/my-app/process/CheckoutFlow
-   → Step 3: validatePayment → calls fetchRates (external)
-
-4. Root cause: fetchRates calls external API without proper timeout
-```
+---
+name: gitnexus-debugging
+description: "Use when the user is debugging a bug, tracing an error, or asking why something fails. Examples: \"Why is X failing?\", \"Where does this error come from?\", \"Trace this bug\""
+---
+
+# Debugging with GitNexus
+
+## When to Use
+
+- "Why is this function failing?"
+- "Trace where this error comes from"
+- "Who calls this method?"
+- "This endpoint returns 500"
+- Investigating bugs, errors, or unexpected behavior
+
+## Workflow
+
+```
+1. gitnexus_query({query: "<error or symptom>"})            → Find related execution flows
+2. gitnexus_context({name: "<suspect>"})                    → See callers/callees/processes
+3. READ gitnexus://repo/{name}/process/{name}                → Trace execution flow
+4. gitnexus_cypher({query: "MATCH path..."})                 → Custom traces if needed
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+
+## Checklist
+
+```
+- [ ] Understand the symptom (error message, unexpected behavior)
+- [ ] gitnexus_query for error text or related code
+- [ ] Identify the suspect function from returned processes
+- [ ] gitnexus_context to see callers and callees
+- [ ] Trace execution flow via process resource if applicable
+- [ ] gitnexus_cypher for custom call chain traces if needed
+- [ ] Read source files to confirm root cause
+```
+
+## Debugging Patterns
+
+| Symptom              | GitNexus Approach                                          |
+| -------------------- | ---------------------------------------------------------- |
+| Error message        | `gitnexus_query` for error text → `context` on throw sites |
+| Wrong return value   | `context` on the function → trace callees for data flow    |
+| Intermittent failure | `context` → look for external calls, async deps            |
+| Performance issue    | `context` → find symbols with many callers (hot paths)     |
+| Recent regression    | `detect_changes` to see what your changes affect           |
+
+## Tools
+
+**gitnexus_query** — find code related to error:
+
+```
+gitnexus_query({query: "payment validation error"})
+→ Processes: CheckoutFlow, ErrorHandling
+→ Symbols: validatePayment, handlePaymentError, PaymentException
+```
+
+**gitnexus_context** — full context for a suspect:
+
+```
+gitnexus_context({name: "validatePayment"})
+→ Incoming calls: processCheckout, webhookHandler
+→ Outgoing calls: verifyCard, fetchRates (external API!)
+→ Processes: CheckoutFlow (step 3/7)
+```
+
+**gitnexus_cypher** — custom call chain traces:
+
+```cypher
+MATCH path = (a)-[:CodeRelation {type: 'CALLS'}*1..2]->(b:Function {name: "validatePayment"})
+RETURN [n IN nodes(path) | n.name] AS chain
+```
+
+## Example: "Payment endpoint returns 500 intermittently"
+
+```
+1. gitnexus_query({query: "payment error handling"})
+   → Processes: CheckoutFlow, ErrorHandling
+   → Symbols: validatePayment, handlePaymentError
+
+2. gitnexus_context({name: "validatePayment"})
+   → Outgoing calls: verifyCard, fetchRates (external API!)
+
+3. READ gitnexus://repo/my-app/process/CheckoutFlow
+   → Step 3: validatePayment → calls fetchRates (external)
+
+4. Root cause: fetchRates calls external API without proper timeout
+```

.claude/skills/gitnexus/gitnexus-exploring/SKILL.md

@@ -1,78 +1,78 @@
----
-name: gitnexus-exploring
-description: "Use when the user asks how code works, wants to understand architecture, trace execution flows, or explore unfamiliar parts of the codebase. Examples: \"How does X work?\", \"What calls this function?\", \"Show me the auth flow\""
----
-
-# Exploring Codebases with GitNexus
-
-## When to Use
-
-- "How does authentication work?"
-- "What's the project structure?"
-- "Show me the main components"
-- "Where is the database logic?"
-- Understanding code you haven't seen before
-
-## Workflow
-
-```
-1. READ gitnexus://repos                          → Discover indexed repos
-2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
-3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
-4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
-5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
-```
-
-> If step 2 says "Index is stale" → run `npx gitnexus analyze` in terminal.
-
-## Checklist
-
-```
-- [ ] READ gitnexus://repo/{name}/context
-- [ ] gitnexus_query for the concept you want to understand
-- [ ] Review returned processes (execution flows)
-- [ ] gitnexus_context on key symbols for callers/callees
-- [ ] READ process resource for full execution traces
-- [ ] Read source files for implementation details
-```
-
-## Resources
-
-| Resource                                | What you get                                            |
-| --------------------------------------- | ------------------------------------------------------- |
-| `gitnexus://repo/{name}/context`        | Stats, staleness warning (~150 tokens)                  |
-| `gitnexus://repo/{name}/clusters`       | All functional areas with cohesion scores (~300 tokens) |
-| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens)              |
-| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens)              |
-
-## Tools
-
-**gitnexus_query** — find execution flows related to a concept:
-
-```
-gitnexus_query({query: "payment processing"})
-→ Processes: CheckoutFlow, RefundFlow, WebhookHandler
-→ Symbols grouped by flow with file locations
-```
-
-**gitnexus_context** — 360-degree view of a symbol:
-
-```
-gitnexus_context({name: "validateUser"})
-→ Incoming calls: loginHandler, apiMiddleware
-→ Outgoing calls: checkToken, getUserById
-→ Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
-```
-
-## Example: "How does payment processing work?"
-
-```
-1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
-2. gitnexus_query({query: "payment processing"})
-   → CheckoutFlow: processPayment → validateCard → chargeStripe
-   → RefundFlow: initiateRefund → calculateRefund → processRefund
-3. gitnexus_context({name: "processPayment"})
-   → Incoming: checkoutHandler, webhookHandler
-   → Outgoing: validateCard, chargeStripe, saveTransaction
-4. Read src/payments/processor.ts for implementation details
-```
+---
+name: gitnexus-exploring
+description: "Use when the user asks how code works, wants to understand architecture, trace execution flows, or explore unfamiliar parts of the codebase. Examples: \"How does X work?\", \"What calls this function?\", \"Show me the auth flow\""
+---
+
+# Exploring Codebases with GitNexus
+
+## When to Use
+
+- "How does authentication work?"
+- "What's the project structure?"
+- "Show me the main components"
+- "Where is the database logic?"
+- Understanding code you haven't seen before
+
+## Workflow
+
+```
+1. READ gitnexus://repos                          → Discover indexed repos
+2. READ gitnexus://repo/{name}/context             → Codebase overview, check staleness
+3. gitnexus_query({query: "<what you want to understand>"})  → Find related execution flows
+4. gitnexus_context({name: "<symbol>"})            → Deep dive on specific symbol
+5. READ gitnexus://repo/{name}/process/{name}      → Trace full execution flow
+```
+
+> If step 2 says "Index is stale" → run `npx gitnexus analyze` in terminal.
+
+## Checklist
+
+```
+- [ ] READ gitnexus://repo/{name}/context
+- [ ] gitnexus_query for the concept you want to understand
+- [ ] Review returned processes (execution flows)
+- [ ] gitnexus_context on key symbols for callers/callees
+- [ ] READ process resource for full execution traces
+- [ ] Read source files for implementation details
+```
+
+## Resources
+
+| Resource                                | What you get                                            |
+| --------------------------------------- | ------------------------------------------------------- |
+| `gitnexus://repo/{name}/context`        | Stats, staleness warning (~150 tokens)                  |
+| `gitnexus://repo/{name}/clusters`       | All functional areas with cohesion scores (~300 tokens) |
+| `gitnexus://repo/{name}/cluster/{name}` | Area members with file paths (~500 tokens)              |
+| `gitnexus://repo/{name}/process/{name}` | Step-by-step execution trace (~200 tokens)              |
+
+## Tools
+
+**gitnexus_query** — find execution flows related to a concept:
+
+```
+gitnexus_query({query: "payment processing"})
+→ Processes: CheckoutFlow, RefundFlow, WebhookHandler
+→ Symbols grouped by flow with file locations
+```
+
+**gitnexus_context** — 360-degree view of a symbol:
+
+```
+gitnexus_context({name: "validateUser"})
+→ Incoming calls: loginHandler, apiMiddleware
+→ Outgoing calls: checkToken, getUserById
+→ Processes: LoginFlow (step 2/5), TokenRefresh (step 1/3)
+```
+
+## Example: "How does payment processing work?"
+
+```
+1. READ gitnexus://repo/my-app/context       → 918 symbols, 45 processes
+2. gitnexus_query({query: "payment processing"})
+   → CheckoutFlow: processPayment → validateCard → chargeStripe
+   → RefundFlow: initiateRefund → calculateRefund → processRefund
+3. gitnexus_context({name: "processPayment"})
+   → Incoming: checkoutHandler, webhookHandler
+   → Outgoing: validateCard, chargeStripe, saveTransaction
+4. Read src/payments/processor.ts for implementation details
+```

.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md

@@ -1,97 +1,97 @@
----
-name: gitnexus-impact-analysis
-description: "Use when the user wants to know what will break if they change something, or needs safety analysis before editing code. Examples: \"Is it safe to change X?\", \"What depends on this?\", \"What will break?\""
----
-
-# Impact Analysis with GitNexus
-
-## When to Use
-
-- "Is it safe to change this function?"
-- "What will break if I modify X?"
-- "Show me the blast radius"
-- "Who uses this code?"
-- Before making non-trivial code changes
-- Before committing — to understand what your changes affect
-
-## Workflow
-
-```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
-2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
-3. gitnexus_detect_changes()                               → Map current git changes to affected flows
-4. Assess risk and report to user
-```
-
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
-
-## Checklist
-
-```
-- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
-- [ ] Review d=1 items first (these WILL BREAK)
-- [ ] Check high-confidence (>0.8) dependencies
-- [ ] READ processes to check affected execution flows
-- [ ] gitnexus_detect_changes() for pre-commit check
-- [ ] Assess risk level and report to user
-```
-
-## Understanding Output
-
-| Depth | Risk Level       | Meaning                  |
-| ----- | ---------------- | ------------------------ |
-| d=1   | **WILL BREAK**   | Direct callers/importers |
-| d=2   | LIKELY AFFECTED  | Indirect dependencies    |
-| d=3   | MAY NEED TESTING | Transitive effects       |
-
-## Risk Assessment
-
-| Affected                       | Risk     |
-| ------------------------------ | -------- |
-| <5 symbols, few processes      | LOW      |
-| 5-15 symbols, 2-5 processes    | MEDIUM   |
-| >15 symbols or many processes  | HIGH     |
-| Critical path (auth, payments) | CRITICAL |
-
-## Tools
-
-**gitnexus_impact** — the primary tool for symbol blast radius:
-
-```
-gitnexus_impact({
-  target: "validateUser",
-  direction: "upstream",
-  minConfidence: 0.8,
-  maxDepth: 3
-})
-
-→ d=1 (WILL BREAK):
-  - loginHandler (src/auth/login.ts:42) [CALLS, 100%]
-  - apiMiddleware (src/api/middleware.ts:15) [CALLS, 100%]
-
-→ d=2 (LIKELY AFFECTED):
-  - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
-```
-
-**gitnexus_detect_changes** — git-diff based impact analysis:
-
-```
-gitnexus_detect_changes({scope: "staged"})
-
-→ Changed: 5 symbols in 3 files
-→ Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
-→ Risk: MEDIUM
-```
-
-## Example: "What breaks if I change validateUser?"
-
-```
-1. gitnexus_impact({target: "validateUser", direction: "upstream"})
-   → d=1: loginHandler, apiMiddleware (WILL BREAK)
-   → d=2: authRouter, sessionManager (LIKELY AFFECTED)
-
-2. READ gitnexus://repo/my-app/processes
-   → LoginFlow and TokenRefresh touch validateUser
-
-3. Risk: 2 direct callers, 2 processes = MEDIUM
-```
+---
+name: gitnexus-impact-analysis
+description: "Use when the user wants to know what will break if they change something, or needs safety analysis before editing code. Examples: \"Is it safe to change X?\", \"What depends on this?\", \"What will break?\""
+---
+
+# Impact Analysis with GitNexus
+
+## When to Use
+
+- "Is it safe to change this function?"
+- "What will break if I modify X?"
+- "Show me the blast radius"
+- "Who uses this code?"
+- Before making non-trivial code changes
+- Before committing — to understand what your changes affect
+
+## Workflow
+
+```
+1. gitnexus_impact({target: "X", direction: "upstream"})  → What depends on this
+2. READ gitnexus://repo/{name}/processes                   → Check affected execution flows
+3. gitnexus_detect_changes()                               → Map current git changes to affected flows
+4. Assess risk and report to user
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+
+## Checklist
+
+```
+- [ ] gitnexus_impact({target, direction: "upstream"}) to find dependents
+- [ ] Review d=1 items first (these WILL BREAK)
+- [ ] Check high-confidence (>0.8) dependencies
+- [ ] READ processes to check affected execution flows
+- [ ] gitnexus_detect_changes() for pre-commit check
+- [ ] Assess risk level and report to user
+```
+
+## Understanding Output
+
+| Depth | Risk Level       | Meaning                  |
+| ----- | ---------------- | ------------------------ |
+| d=1   | **WILL BREAK**   | Direct callers/importers |
+| d=2   | LIKELY AFFECTED  | Indirect dependencies    |
+| d=3   | MAY NEED TESTING | Transitive effects       |
+
+## Risk Assessment
+
+| Affected                       | Risk     |
+| ------------------------------ | -------- |
+| <5 symbols, few processes      | LOW      |
+| 5-15 symbols, 2-5 processes    | MEDIUM   |
+| >15 symbols or many processes  | HIGH     |
+| Critical path (auth, payments) | CRITICAL |
+
+## Tools
+
+**gitnexus_impact** — the primary tool for symbol blast radius:
+
+```
+gitnexus_impact({
+  target: "validateUser",
+  direction: "upstream",
+  minConfidence: 0.8,
+  maxDepth: 3
+})
+
+→ d=1 (WILL BREAK):
+  - loginHandler (src/auth/login.ts:42) [CALLS, 100%]
+  - apiMiddleware (src/api/middleware.ts:15) [CALLS, 100%]
+
+→ d=2 (LIKELY AFFECTED):
+  - authRouter (src/routes/auth.ts:22) [CALLS, 95%]
+```
+
+**gitnexus_detect_changes** — git-diff based impact analysis:
+
+```
+gitnexus_detect_changes({scope: "staged"})
+
+→ Changed: 5 symbols in 3 files
+→ Affected: LoginFlow, TokenRefresh, APIMiddlewarePipeline
+→ Risk: MEDIUM
+```
+
+## Example: "What breaks if I change validateUser?"
+
+```
+1. gitnexus_impact({target: "validateUser", direction: "upstream"})
+   → d=1: loginHandler, apiMiddleware (WILL BREAK)
+   → d=2: authRouter, sessionManager (LIKELY AFFECTED)
+
+2. READ gitnexus://repo/my-app/processes
+   → LoginFlow and TokenRefresh touch validateUser
+
+3. Risk: 2 direct callers, 2 processes = MEDIUM
+```

.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md

@@ -1,121 +1,121 @@
----
-name: gitnexus-refactoring
-description: "Use when the user wants to rename, extract, split, move, or restructure code safely. Examples: \"Rename this function\", \"Extract this into a module\", \"Refactor this class\", \"Move this to a separate file\""
----
-
-# Refactoring with GitNexus
-
-## When to Use
-
-- "Rename this function safely"
-- "Extract this into a module"
-- "Split this service"
-- "Move this to a new file"
-- Any task involving renaming, extracting, splitting, or restructuring code
-
-## Workflow
-
-```
-1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
-2. gitnexus_query({query: "X"})                            → Find execution flows involving X
-3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
-4. Plan update order: interfaces → implementations → callers → tests
-```
-
-> If "Index is stale" → run `npx gitnexus analyze` in terminal.
-
-## Checklists
-
-### Rename Symbol
-
-```
-- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
-- [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
-- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
-- [ ] gitnexus_detect_changes() — verify only expected files changed
-- [ ] Run tests for affected processes
-```
-
-### Extract Module
-
-```
-- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
-- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
-- [ ] Define new module interface
-- [ ] Extract code, update imports
-- [ ] gitnexus_detect_changes() — verify affected scope
-- [ ] Run tests for affected processes
-```
-
-### Split Function/Service
-
-```
-- [ ] gitnexus_context({name: target}) — understand all callees
-- [ ] Group callees by responsibility
-- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
-- [ ] Create new functions/services
-- [ ] Update callers
-- [ ] gitnexus_detect_changes() — verify affected scope
-- [ ] Run tests for affected processes
-```
-
-## Tools
-
-**gitnexus_rename** — automated multi-file rename:
-
-```
-gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
-→ 12 edits across 8 files
-→ 10 graph edits (high confidence), 2 ast_search edits (review)
-→ Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
-```
-
-**gitnexus_impact** — map all dependents first:
-
-```
-gitnexus_impact({target: "validateUser", direction: "upstream"})
-→ d=1: loginHandler, apiMiddleware, testUtils
-→ Affected Processes: LoginFlow, TokenRefresh
-```
-
-**gitnexus_detect_changes** — verify your changes after refactoring:
-
-```
-gitnexus_detect_changes({scope: "all"})
-→ Changed: 8 files, 12 symbols
-→ Affected processes: LoginFlow, TokenRefresh
-→ Risk: MEDIUM
-```
-
-**gitnexus_cypher** — custom reference queries:
-
-```cypher
-MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
-RETURN caller.name, caller.filePath ORDER BY caller.filePath
-```
-
-## Risk Rules
-
-| Risk Factor         | Mitigation                                |
-| ------------------- | ----------------------------------------- |
-| Many callers (>5)   | Use gitnexus_rename for automated updates |
-| Cross-area refs     | Use detect_changes after to verify scope  |
-| String/dynamic refs | gitnexus_query to find them               |
-| External/public API | Version and deprecate properly            |
-
-## Example: Rename `validateUser` to `authenticateUser`
-
-```
-1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
-   → 12 edits: 10 graph (safe), 2 ast_search (review)
-   → Files: validator.ts, login.ts, middleware.ts, config.json...
-
-2. Review ast_search edits (config.json: dynamic reference!)
-
-3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
-   → Applied 12 edits across 8 files
-
-4. gitnexus_detect_changes({scope: "all"})
-   → Affected: LoginFlow, TokenRefresh
-   → Risk: MEDIUM — run tests for these flows
-```
+---
+name: gitnexus-refactoring
+description: "Use when the user wants to rename, extract, split, move, or restructure code safely. Examples: \"Rename this function\", \"Extract this into a module\", \"Refactor this class\", \"Move this to a separate file\""
+---
+
+# Refactoring with GitNexus
+
+## When to Use
+
+- "Rename this function safely"
+- "Extract this into a module"
+- "Split this service"
+- "Move this to a new file"
+- Any task involving renaming, extracting, splitting, or restructuring code
+
+## Workflow
+
+```
+1. gitnexus_impact({target: "X", direction: "upstream"})  → Map all dependents
+2. gitnexus_query({query: "X"})                            → Find execution flows involving X
+3. gitnexus_context({name: "X"})                           → See all incoming/outgoing refs
+4. Plan update order: interfaces → implementations → callers → tests
+```
+
+> If "Index is stale" → run `npx gitnexus analyze` in terminal.
+
+## Checklists
+
+### Rename Symbol
+
+```
+- [ ] gitnexus_rename({symbol_name: "oldName", new_name: "newName", dry_run: true}) — preview all edits
+- [ ] Review graph edits (high confidence) and ast_search edits (review carefully)
+- [ ] If satisfied: gitnexus_rename({..., dry_run: false}) — apply edits
+- [ ] gitnexus_detect_changes() — verify only expected files changed
+- [ ] Run tests for affected processes
+```
+
+### Extract Module
+
+```
+- [ ] gitnexus_context({name: target}) — see all incoming/outgoing refs
+- [ ] gitnexus_impact({target, direction: "upstream"}) — find all external callers
+- [ ] Define new module interface
+- [ ] Extract code, update imports
+- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] Run tests for affected processes
+```
+
+### Split Function/Service
+
+```
+- [ ] gitnexus_context({name: target}) — understand all callees
+- [ ] Group callees by responsibility
+- [ ] gitnexus_impact({target, direction: "upstream"}) — map callers to update
+- [ ] Create new functions/services
+- [ ] Update callers
+- [ ] gitnexus_detect_changes() — verify affected scope
+- [ ] Run tests for affected processes
+```
+
+## Tools
+
+**gitnexus_rename** — automated multi-file rename:
+
+```
+gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+→ 12 edits across 8 files
+→ 10 graph edits (high confidence), 2 ast_search edits (review)
+→ Changes: [{file_path, edits: [{line, old_text, new_text, confidence}]}]
+```
+
+**gitnexus_impact** — map all dependents first:
+
+```
+gitnexus_impact({target: "validateUser", direction: "upstream"})
+→ d=1: loginHandler, apiMiddleware, testUtils
+→ Affected Processes: LoginFlow, TokenRefresh
+```
+
+**gitnexus_detect_changes** — verify your changes after refactoring:
+
+```
+gitnexus_detect_changes({scope: "all"})
+→ Changed: 8 files, 12 symbols
+→ Affected processes: LoginFlow, TokenRefresh
+→ Risk: MEDIUM
+```
+
+**gitnexus_cypher** — custom reference queries:
+
+```cypher
+MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "validateUser"})
+RETURN caller.name, caller.filePath ORDER BY caller.filePath
+```
+
+## Risk Rules
+
+| Risk Factor         | Mitigation                                |
+| ------------------- | ----------------------------------------- |
+| Many callers (>5)   | Use gitnexus_rename for automated updates |
+| Cross-area refs     | Use detect_changes after to verify scope  |
+| String/dynamic refs | gitnexus_query to find them               |
+| External/public API | Version and deprecate properly            |
+
+## Example: Rename `validateUser` to `authenticateUser`
+
+```
+1. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: true})
+   → 12 edits: 10 graph (safe), 2 ast_search (review)
+   → Files: validator.ts, login.ts, middleware.ts, config.json...
+
+2. Review ast_search edits (config.json: dynamic reference!)
+
+3. gitnexus_rename({symbol_name: "validateUser", new_name: "authenticateUser", dry_run: false})
+   → Applied 12 edits across 8 files
+
+4. gitnexus_detect_changes({scope: "all"})
+   → Affected: LoginFlow, TokenRefresh
+   → Risk: MEDIUM — run tests for these flows
+```

.github/actions/setup-gitnexus/action.yml

@@ -1,28 +0,0 @@
-name: Setup GitNexus
-description: Setup Node.js 20, install dependencies, and optionally build
-
-inputs:
-  build:
-    description: Whether to run npm run build after install
-    required: false
-    default: 'false'
-
-runs:
-  using: composite
-  steps:
-    - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
-      with:
-        node-version: 20
-        cache: npm
-        cache-dependency-path: gitnexus/package-lock.json
-
-    - name: Install dependencies
-      run: npm ci
-      shell: bash
-      working-directory: gitnexus
-
-    - name: Build
-      if: ${{ inputs.build == 'true' }}
-      run: npm run build
-      shell: bash
-      working-directory: gitnexus

.github/release.yml

@@ -1,45 +0,0 @@
-changelog:
-  exclude:
-    labels:
-      - chore
-    authors:
-      - dependabot
-      - dependabot[bot]
-  categories:
-    - title: "\U0001F6A8 Security"
-      labels:
-        - security
-    - title: "\U0001F4A5 Breaking Changes"
-      labels:
-        - breaking
-    - title: "\U0001F680 Features"
-      labels:
-        - enhancement
-    - title: "\U0001F41B Bug Fixes"
-      labels:
-        - bug
-    - title: "\U0001F3CE\uFE0F Performance"
-      labels:
-        - performance
-    - title: "\U0001F9EA Tests"
-      labels:
-        - test
-    - title: "\U0001F504 Refactoring"
-      labels:
-        - refactor
-    - title: "\U0001F477 CI/CD"
-      labels:
-        - ci
-    - title: "\U0001F4E6 Dependencies"
-      labels:
-        - dependencies
-    - title: "\U0001F4DD Other Changes"
-      labels:
-        - "*"
-      exclude:
-        labels:
-          - dependencies
-          - ci
-          - test
-          - refactor
-          - chore

.github/scripts/triage/embedding_utils.py

@@ -1,257 +0,0 @@
-"""Pure math utilities for triage sweep embedding analysis.
-
-All functions are stateless and perform no I/O (except model loading by FastEmbed).
-Each function operates on numpy arrays and returns numpy arrays or plain Python types.
-"""
-from __future__ import annotations
-
-import numpy as np
-from numpy.typing import NDArray
-from fastembed import TextEmbedding
-from sklearn.decomposition import PCA
-from sklearn.covariance import EllipticEnvelope
-from sklearn.metrics.pairwise import cosine_similarity
-
-# FastEmbed model — BAAI/bge-small-en-v1.5 produces 384-dimensional embeddings.
-# ~46MB quantized ONNX, runs on CPU in ~0.5s per batch of 32.
-EMBEDDING_MODEL: str = "BAAI/bge-small-en-v1.5"
-
-# Embedding dimensionality (determined by model choice).
-EMBEDDING_DIM: int = 384
-
-# Batch size for FastEmbed. 32 balances memory and throughput on
-# a 2-vCPU GitHub Actions runner with ~7GB RAM.
-EMBEDDING_BATCH_SIZE: int = 32
-
-
-def embed_texts(texts: list[str]) -> NDArray[np.float32]:
-    """Embed a list of texts into dense vectors using FastEmbed.
-
-    Returns an array of shape (len(texts), 384) with dtype float32.
-    Empty input returns a (0, 384) array.
-    """
-    if not texts:
-        return np.empty((0, EMBEDDING_DIM), dtype=np.float32)
-
-    model = TextEmbedding(model_name=EMBEDDING_MODEL)
-    vectors = list(model.embed(texts, batch_size=EMBEDDING_BATCH_SIZE))
-    return np.vstack(vectors).astype(np.float32)
-
-
-def normalize_rows(matrix: NDArray[np.float32]) -> NDArray[np.float32]:
-    """L2-normalize each row to unit length.
-
-    Zero-norm rows (e.g. from empty text) remain zero vectors.
-    Uses eps=1e-10 in the denominator to avoid division by zero.
-    """
-    if matrix.shape[0] == 0:
-        return matrix
-
-    norms = np.linalg.norm(matrix, axis=1, keepdims=True)
-    return matrix / (norms + 1e-10)
-
-
-def reduce_dimensions(
-    matrix: NDArray[np.float32],
-    max_components: int,
-) -> NDArray[np.float32]:
-    """Reduce dimensionality via PCA.
-
-    Computes n_components = min(max_components, n-1, d). If n_components < 1,
-    returns the matrix unchanged. Logs explained variance for observability.
-    """
-    n, d = matrix.shape
-    if n <= 1:
-        return matrix
-
-    n_components = min(max_components, n - 1, d)
-    if n_components < 1:
-        return matrix
-
-    pca = PCA(n_components=n_components)
-    reduced = pca.fit_transform(matrix)
-    explained = pca.explained_variance_ratio_.sum()
-    print(f"PCA: {d}d -> {n_components}d, explained variance: {explained:.3f}")
-    return reduced.astype(np.float32)
-
-
-def detect_outliers(
-    matrix: NDArray[np.float32],
-    contamination: float = 0.1,
-    iqr_multiplier: float = 3.0,
-    max_outlier_pct: float = 0.05,
-) -> list[tuple[int, float]]:
-    """Flag items whose Mahalanobis distance exceeds an IQR-based cutoff.
-
-    Uses EllipticEnvelope (robust covariance via MCD) to estimate the
-    multivariate Gaussian, then computes sqrt(squared Mahalanobis distance)
-    for each sample. The cutoff is Q75 + iqr_multiplier * IQR, which
-    adapts to the actual distribution of distances.
-
-    A hard cap ensures no more than max_outlier_pct * n items are flagged;
-    when the cap is hit, only the most extreme items (sorted by distance
-    descending) are kept.
-
-    Returns (index, distance) tuples sorted by index ascending, along with
-    the cutoff value stored as an attribute on the returned list.
-    """
-    n = matrix.shape[0]
-    if n < 2:
-        return []
-
-    envelope = EllipticEnvelope(contamination=contamination, random_state=42)
-    envelope.fit(matrix)
-
-    # .mahalanobis() returns squared Mahalanobis distances
-    distances = np.sqrt(envelope.mahalanobis(matrix))
-
-    # IQR-based cutoff
-    q25, q75 = np.percentile(distances, [25, 75])
-    iqr = q75 - q25
-    cutoff = q75 + iqr_multiplier * iqr
-
-    outlier_mask = distances > cutoff
-    indices = np.where(outlier_mask)[0]
-
-    # Hard cap: keep at most max_outlier_pct * n items
-    max_count = max(1, int(max_outlier_pct * n))
-    if len(indices) > max_count:
-        # Sort by distance descending, take the most extreme
-        sorted_by_dist = sorted(indices, key=lambda i: distances[i], reverse=True)
-        indices = np.array(sorted_by_dist[:max_count])
-
-    # Sort by index ascending for stable output
-    indices = np.sort(indices)
-    result = [(int(idx), float(distances[idx])) for idx in indices]
-
-    # Attach cutoff as metadata so the report can use it
-    result = _OutlierResult(result)  # type: ignore[assignment]
-    result.cutoff = float(cutoff)  # type: ignore[attr-defined]
-    return result  # type: ignore[return-value]
-
-
-class _OutlierResult(list):
-    """A list subclass that carries metadata (cutoff) from outlier detection."""
-    cutoff: float = 0.0
-
-
-def find_duplicate_pairs(
-    matrix: NDArray[np.float32],
-    threshold: float,
-) -> list[tuple[int, int, float]]:
-    """Find pairs of items with cosine similarity above threshold.
-
-    Returns (i, j, similarity) tuples where i < j. The input should be
-    L2-normalized embeddings (full dimensionality, not PCA-reduced) so
-    cosine similarity equals the dot product.
-    """
-    n = matrix.shape[0]
-    if n <= 1:
-        return []
-
-    sim_matrix = cosine_similarity(matrix)
-    # Upper triangle indices (i < j), excluding diagonal
-    rows, cols = np.triu_indices(n, k=1)
-    similarities = sim_matrix[rows, cols]
-
-    mask = similarities > threshold
-    pairs: list[tuple[int, int, float]] = []
-    for idx in np.where(mask)[0]:
-        pairs.append((int(rows[idx]), int(cols[idx]), float(similarities[idx])))
-
-    return pairs
-
-
-# ── Label suggestion via z-score normalized embedding similarity ──────
-
-# Z-score threshold: a label must be this many standard deviations above
-# the column mean to be considered a match.
-LABEL_Z_THRESHOLD: float = 1.5
-
-# Margin gate: the top-1 label must beat the second-best by this many
-# z-score units to be accepted (subsequent labels don't need a margin).
-LABEL_Z_MARGIN: float = 0.5
-
-# Floor for per-column standard deviation to avoid division by near-zero.
-LABEL_Z_STD_FLOOR: float = 0.01
-
-# Minimum raw cosine similarity required even if z-score is high.
-# Prevents suggesting labels that are "relatively best" but still poor.
-MIN_RAW_SIMILARITY: float = 0.3
-
-# Maximum number of labels to suggest per item.
-MAX_LABELS_PER_ITEM: int = 3
-
-
-def suggest_labels(
-    item_embeddings: NDArray[np.float32],
-    label_embeddings: NDArray[np.float32],
-    label_names: list[str],
-    z_threshold: float = LABEL_Z_THRESHOLD,
-    z_margin: float = LABEL_Z_MARGIN,
-    std_floor: float = LABEL_Z_STD_FLOOR,
-    min_raw_sim: float = MIN_RAW_SIMILARITY,
-    max_per_item: int = MAX_LABELS_PER_ITEM,
-) -> list[list[tuple[str, float]]]:
-    """Suggest labels for each item using z-score normalized similarity.
-
-    1. Compute raw cosine similarity matrix (n items x m labels).
-    2. Column-wise z-score: for each label j, normalize across all items.
-    3. For each item, rank labels by z-score descending.
-    4. Accept a label only if z >= z_threshold AND raw_sim >= min_raw_sim.
-    5. Margin gate: the top-1 label must beat #2 by z_margin; subsequent
-       labels don't need a margin.
-    6. Cap at max_per_item.
-
-    Returns a list of length n, where each element is a list of
-    (label_name, raw_similarity) tuples. Empty list if nothing qualifies.
-    """
-    n = item_embeddings.shape[0]
-    m = label_embeddings.shape[0]
-    if n == 0 or m == 0:
-        return [[] for _ in range(n)]
-
-    # (n, m) raw similarity matrix
-    sim_matrix = cosine_similarity(item_embeddings, label_embeddings)
-
-    # Column-wise z-score normalization
-    col_means = sim_matrix.mean(axis=0)  # shape (m,)
-    col_stds = sim_matrix.std(axis=0)    # shape (m,)
-    col_stds = np.maximum(col_stds, std_floor)
-    z_matrix = (sim_matrix - col_means) / col_stds
-
-    suggestions: list[list[tuple[str, float]]] = []
-    for i in range(n):
-        z_row = z_matrix[i]
-        raw_row = sim_matrix[i]
-
-        # Rank labels by z-score descending
-        ranked = np.argsort(z_row)[::-1]
-
-        item_labels: list[tuple[str, float]] = []
-
-        # Margin gate: top-1 z-score must beat #2 by z_margin.
-        # If not, the assignment is ambiguous — skip this item entirely.
-        if len(ranked) > 1:
-            top1_z = float(z_row[ranked[0]])
-            top2_z = float(z_row[ranked[1]])
-            if top1_z - top2_z < z_margin:
-                suggestions.append(item_labels)
-                continue
-
-        for rank_pos, idx in enumerate(ranked):
-            if len(item_labels) >= max_per_item:
-                break
-
-            z_val = float(z_row[idx])
-            raw_val = float(raw_row[idx])
-
-            # Must pass both z-threshold and raw similarity floor
-            if z_val < z_threshold or raw_val < min_raw_sim:
-                continue
-
-            item_labels.append((label_names[idx], raw_val))
-
-        suggestions.append(item_labels)
-
-    return suggestions

.github/scripts/triage/requirements.txt

@@ -1,4 +0,0 @@
-fastembed>=0.5.0
-numpy>=1.26.0
-scikit-learn>=1.4.0
-scipy>=1.10.0

.github/scripts/triage/sweep.py

@@ -1,600 +0,0 @@
-"""Triage sweep: fetch open issues/PRs, detect outliers and duplicates, generate a report.
-
-Entrypoint script for the triage-sweep workflow. Fetches all open items via
-the GitHub REST API, delegates embedding and analysis to embedding_utils,
-generates a markdown report, and optionally creates a report issue.
-"""
-from __future__ import annotations
-
-import json
-import os
-import sys
-import urllib.request
-import urllib.parse
-from typing import TypedDict
-from datetime import datetime, timezone
-
-from embedding_utils import (
-    embed_texts,
-    normalize_rows,
-    reduce_dimensions,
-    detect_outliers,
-    find_duplicate_pairs,
-    suggest_labels,
-    LABEL_Z_THRESHOLD,
-    LABEL_Z_MARGIN,
-    LABEL_Z_STD_FLOOR,
-    MIN_RAW_SIMILARITY,
-    MAX_LABELS_PER_ITEM,
-)
-
-# ── Thresholds (overridable via workflow_dispatch inputs) ──────────────
-
-# IQR multiplier for outlier cutoff: cutoff = Q75 + IQR_MULTIPLIER * IQR.
-IQR_MULTIPLIER: float = float(os.environ.get("INPUT_IQR_MULTIPLIER", "3.0"))
-
-# Hard cap: at most this fraction of items can be flagged as outliers.
-MAX_OUTLIER_PCT: float = float(os.environ.get("INPUT_MAX_OUTLIER_PCT", "0.05"))
-
-# EllipticEnvelope contamination: expected fraction of outliers in the data.
-# Governs how aggressively the robust covariance downweights extreme points.
-CONTAMINATION: float = float(os.environ.get("INPUT_CONTAMINATION", "0.1"))
-
-# Cosine similarity above which two items are flagged as duplicates.
-# 0.92 catches near-identical issues while tolerating paraphrasing.
-COSINE_THRESHOLD: float = float(os.environ.get("INPUT_COSINE_THRESHOLD", "0.92"))
-
-# Hard cap on items to process. Prevents runaway costs on very large repos.
-MAX_ITEMS: int = int(os.environ.get("INPUT_MAX_ITEMS", "500"))
-
-# When true, print report to stdout/file but do not create a GitHub issue.
-DRY_RUN: bool = os.environ.get("INPUT_DRY_RUN", "false").lower() == "true"
-
-# ── Fixed constants (not user-configurable) ───────────────────────────
-
-# Minimum number of samples required for EllipticEnvelope to fit
-# a Gaussian reliably. Must be >= 3 * PCA_MAX_COMPONENTS so the
-# covariance matrix is estimated from enough data points.
-PCA_MAX_COMPONENTS: int = 20
-MIN_SAMPLES_FOR_OUTLIER_DETECTION: int = 100
-
-# Max character length for embedding input text. bge-small-en-v1.5 has a
-# 512-token context window (~4 chars/token). We keep title + body under
-# this limit so the model sees the full text instead of silently truncating.
-MAX_EMBED_CHARS: int = 2000
-
-# GitHub REST API page size (max allowed is 100).
-API_PAGE_SIZE: int = 100
-
-# Report issue label.
-REPORT_LABEL: str = "triage-report"
-
-# Report file path (written for the summary step to pick up).
-REPORT_FILE: str = "/tmp/triage-report.md"
-
-
-class TriageItem(TypedDict):
-    """One open issue or PR, with only the fields we need."""
-    number: int
-    title: str
-    html_url: str
-    is_pr: bool
-    labels: list[str]
-    created_at: str
-    # title + body concatenated, used as embedding input
-    text: str
-
-
-def github_api_get(path: str) -> list[dict]:
-    """Make a single authenticated GET request to the GitHub REST API.
-
-    Reads GITHUB_TOKEN and GITHUB_REPOSITORY from env. Raises SystemExit
-    with the HTTP status and response body on any non-2xx response.
-    """
-    token = os.environ["GITHUB_TOKEN"]
-    repo = os.environ["GITHUB_REPOSITORY"]
-    url = f"https://api.github.com/repos/{repo}{path}"
-
-    req = urllib.request.Request(url)
-    req.add_header("Accept", "application/vnd.github+json")
-    req.add_header("Authorization", f"Bearer {token}")
-    req.add_header("X-GitHub-Api-Version", "2022-11-28")
-
-    try:
-        with urllib.request.urlopen(req, timeout=30) as resp:
-            return json.loads(resp.read().decode("utf-8"))
-    except urllib.error.HTTPError as e:
-        body = e.read().decode("utf-8", errors="replace")
-        print(f"::error::GitHub API {e.code}: {body}")
-        sys.exit(1)
-
-
-def fetch_all_open_items() -> list[TriageItem]:
-    """Paginate through all open issues and PRs.
-
-    Returns up to MAX_ITEMS TriageItem dicts. Items with a pull_request
-    key are marked is_pr=True. The text field is title + body concatenated.
-    """
-    items: list[TriageItem] = []
-    page = 1
-
-    while len(items) < MAX_ITEMS:
-        path = (
-            f"/issues?state=open&per_page={API_PAGE_SIZE}"
-            f"&sort=created&direction=desc&page={page}"
-        )
-        data = github_api_get(path)
-
-        if not data:
-            break
-
-        for raw in data:
-            if len(items) >= MAX_ITEMS:
-                break
-
-            body = raw.get("body", "") or ""
-            full_text = f"{raw['title']}\n\n{body}"
-            # Truncate to fit the embedding model's token window.
-            # Title is always preserved; body gets clipped if needed.
-            if len(full_text) > MAX_EMBED_CHARS:
-                full_text = full_text[:MAX_EMBED_CHARS]
-            items.append(TriageItem(
-                number=raw["number"],
-                title=raw["title"],
-                html_url=raw["html_url"],
-                is_pr="pull_request" in raw,
-                labels=[lbl["name"] for lbl in raw.get("labels", [])],
-                created_at=raw["created_at"],
-                text=full_text,
-            ))
-
-        if len(data) < API_PAGE_SIZE:
-            break
-
-        page += 1
-
-    return items
-
-
-class RepoLabel(TypedDict):
-    """A label from the repo with its embedding text."""
-    name: str
-    description: str
-    # "name: description" concatenated for embedding
-    text: str
-
-
-def fetch_repo_labels() -> list[RepoLabel]:
-    """Fetch all labels from the repository, paginating if needed.
-
-    Returns labels with name, description, and a text field suitable
-    for embedding ("name: description"). Labels with no description
-    use just the name.
-    """
-    labels: list[RepoLabel] = []
-    page = 1
-
-    while True:
-        data = github_api_get(f"/labels?per_page={API_PAGE_SIZE}&page={page}")
-        for raw in data:
-            name = raw["name"]
-            desc = raw.get("description", "") or ""
-            text = f"{name}: {desc}" if desc else name
-            labels.append(RepoLabel(name=name, description=desc, text=text))
-
-        if len(data) < API_PAGE_SIZE:
-            break
-        page += 1
-
-    return labels
-
-
-def apply_labels_to_item(item_number: int, labels: list[str]) -> None:
-    """Add labels to a single issue/PR via the GitHub API.
-
-    Skips silently if labels list is empty. Uses POST which adds labels
-    without removing existing ones.
-    """
-    if not labels:
-        return
-
-    token = os.environ["GITHUB_TOKEN"]
-    repo = os.environ["GITHUB_REPOSITORY"]
-    url = f"https://api.github.com/repos/{repo}/issues/{item_number}/labels"
-
-    payload = json.dumps({"labels": labels}).encode("utf-8")
-    req = urllib.request.Request(url, data=payload, method="POST")
-    req.add_header("Accept", "application/vnd.github+json")
-    req.add_header("Authorization", f"Bearer {token}")
-    req.add_header("X-GitHub-Api-Version", "2022-11-28")
-    req.add_header("Content-Type", "application/json")
-
-    try:
-        with urllib.request.urlopen(req, timeout=30) as resp:
-            resp.read()
-    except urllib.error.HTTPError as e:
-        body = e.read().decode("utf-8", errors="replace")
-        # Non-fatal: log warning but don't abort the sweep
-        print(f"::warning::Failed to label #{item_number}: {e.code} {body}")
-
-
-def _item_age(created_at: str) -> str:
-    """Compute a human-readable age string from an ISO 8601 created_at timestamp."""
-    try:
-        created = datetime.fromisoformat(created_at.replace("Z", "+00:00"))
-        delta = datetime.now(timezone.utc) - created
-        days = delta.days
-        if days < 1:
-            return "<1d"
-        if days < 30:
-            return f"{days}d"
-        if days < 365:
-            return f"{days // 30}mo"
-        return f"{days // 365}y"
-    except (ValueError, TypeError):
-        return "?"
-
-
-def _suggested_action(a: TriageItem, b: TriageItem) -> str:
-    """Determine a suggested action for a duplicate pair based on types and age."""
-    if a["is_pr"] and b["is_pr"]:
-        return "Review for overlap"
-    if not a["is_pr"] and not b["is_pr"]:
-        # Both issues — close the newer one
-        try:
-            a_dt = datetime.fromisoformat(a["created_at"].replace("Z", "+00:00"))
-            b_dt = datetime.fromisoformat(b["created_at"].replace("Z", "+00:00"))
-            newer = b if b_dt > a_dt else a
-        except (ValueError, TypeError):
-            newer = b
-        return f"Close #{newer['number']} as duplicate"
-    # One issue, one PR
-    return "Link PR to issue"
-
-
-def generate_report(
-    items: list[TriageItem],
-    outlier_results: list[tuple[int, float]],
-    duplicate_pairs: list[tuple[int, int, float]],
-    label_suggestions: list[list[tuple[str, float]]] | None = None,
-) -> str:
-    """Generate a structured markdown triage report."""
-    now = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S")
-    repo = os.environ.get("GITHUB_REPOSITORY", "unknown/repo")
-
-    # Compute label suggestion counts early for the health table
-    outlier_set = {idx for idx, _ in outlier_results}
-    suggested_count = 0
-    if label_suggestions is not None:
-        suggested_count = sum(
-            1 for i, s in enumerate(label_suggestions)
-            if s and not items[i]["labels"] and i not in outlier_set
-        )
-
-    # ── Health summary table at the top ──────────────────────────────
-    lines: list[str] = [
-        "## Triage Sweep Report",
-        "",
-        f"**Run:** {now} UTC",
-        f"**Items analyzed:** {len(items)}",
-        f"**Thresholds:** IQR multiplier {IQR_MULTIPLIER}, Cosine > {COSINE_THRESHOLD}",
-        "",
-        "### Health Summary",
-        "",
-        "| Metric | Value |",
-        "|--------|-------|",
-        f"| Items analyzed | {len(items)} |",
-        f"| Outliers flagged | {len(outlier_results)} |",
-        f"| Duplicate pairs | {len(duplicate_pairs)} |",
-        f"| Label suggestions | {suggested_count} |",
-        "",
-    ]
-
-    # ── Outlier section ──────────────────────────────────────────────
-    # Determine cutoff for high-confidence split
-    cutoff = getattr(outlier_results, "cutoff", 0.0)
-    high_conf_cutoff = 2 * cutoff if cutoff > 0 else float("inf")
-
-    high_conf = [(idx, d) for idx, d in outlier_results if d > high_conf_cutoff]
-    borderline = [(idx, d) for idx, d in outlier_results if d <= high_conf_cutoff]
-
-    lines.extend([
-        f"### Potential Outliers / Spam ({len(outlier_results)})",
-        "",
-        "Items with unusually high Mahalanobis distance from the distribution center.",
-        "These may be spam, off-topic, or poorly described.",
-        "",
-    ])
-
-    if high_conf:
-        lines.append(f"**High Confidence** ({len(high_conf)} items, distance > 2x cutoff)")
-        lines.append("")
-        lines.append("| # | Type | Title | Distance | Age |")
-        lines.append("|---|------|-------|----------|-----|")
-        for idx, distance in high_conf:
-            item = items[idx]
-            kind = "PR" if item["is_pr"] else "Issue"
-            age = _item_age(item["created_at"])
-            title = item["title"][:80] + ("..." if len(item["title"]) > 80 else "")
-            lines.append(
-                f"| [#{item['number']}]({item['html_url']}) "
-                f"| {kind} | {title} | {distance:.2f} | {age} |"
-            )
-        lines.append("")
-
-    if borderline:
-        lines.append("<details>")
-        lines.append(f"<summary>Borderline ({len(borderline)} items)</summary>")
-        lines.append("")
-        lines.append("| # | Type | Title | Distance | Age |")
-        lines.append("|---|------|-------|----------|-----|")
-        for idx, distance in borderline:
-            item = items[idx]
-            kind = "PR" if item["is_pr"] else "Issue"
-            age = _item_age(item["created_at"])
-            title = item["title"][:80] + ("..." if len(item["title"]) > 80 else "")
-            lines.append(
-                f"| [#{item['number']}]({item['html_url']}) "
-                f"| {kind} | {title} | {distance:.2f} | {age} |"
-            )
-        lines.append("")
-        lines.append("</details>")
-        lines.append("")
-
-    if not outlier_results:
-        lines.append("None found.")
-
-    # ── Duplicate pairs section ──────────────────────────────────────
-    lines.extend([
-        "",
-        f"### Potential Duplicates ({len(duplicate_pairs)} pairs)",
-        "",
-        "Pairs of items with cosine similarity above the threshold.",
-        "",
-    ])
-
-    if duplicate_pairs:
-        lines.append("| Item A | Item B | Similarity | Suggested Action |")
-        lines.append("|--------|--------|------------|------------------|")
-        for i, j, sim in duplicate_pairs:
-            a = items[i]
-            b = items[j]
-            kind_a = "PR" if a["is_pr"] else "Issue"
-            kind_b = "PR" if b["is_pr"] else "Issue"
-            action = _suggested_action(a, b)
-            lines.append(
-                f"| [#{a['number']}]({a['html_url']}) {kind_a}: {a['title']} "
-                f"| [#{b['number']}]({b['html_url']}) {kind_b}: {b['title']} "
-                f"| {sim:.3f} | {action} |"
-            )
-    else:
-        lines.append("None found.")
-
-    # ── Label suggestions section ────────────────────────────────────
-    if label_suggestions is not None:
-        # High confidence: top-1 label with raw_sim >= 0.5
-        # Low confidence: top-1 label with raw_sim < 0.5
-        high_conf_labels: list[tuple[int, list[tuple[str, float]]]] = []
-        low_conf_labels: list[tuple[int, list[tuple[str, float]]]] = []
-        for i, sugs in enumerate(label_suggestions):
-            if sugs and not items[i]["labels"] and i not in outlier_set:
-                top1 = sugs[:1]
-                if top1[0][1] >= 0.5:
-                    high_conf_labels.append((i, top1))
-                else:
-                    low_conf_labels.append((i, top1))
-
-        total_suggestions = len(high_conf_labels) + len(low_conf_labels)
-        lines.extend([
-            "",
-            f"### Suggested Labels ({total_suggestions} unlabeled items)",
-            "",
-            "Labels suggested by z-score normalized embedding similarity against repo label descriptions.",
-            "Only shown for unlabeled items that were not flagged as outliers.",
-            "",
-        ])
-
-        # Label concentration warning
-        if total_suggestions > 0:
-            label_counts: dict[str, int] = {}
-            for _, sugs in high_conf_labels + low_conf_labels:
-                for name, _ in sugs:
-                    label_counts[name] = label_counts.get(name, 0) + 1
-            for name, count in label_counts.items():
-                if count > total_suggestions * 0.5:
-                    lines.append(
-                        f"> **Warning:** Label `{name}` accounts for "
-                        f"{count}/{total_suggestions} suggestions "
-                        f"({count * 100 // total_suggestions}%). "
-                        f"Consider reviewing label descriptions for specificity."
-                    )
-                    lines.append("")
-
-        if high_conf_labels:
-            lines.append("| # | Type | Title | Suggested Label |")
-            lines.append("|---|------|-------|--------------------|")
-            for idx, sugs in high_conf_labels:
-                item = items[idx]
-                kind = "PR" if item["is_pr"] else "Issue"
-                label_strs = [f"`{name}` ({score:.2f})" for name, score in sugs]
-                lines.append(
-                    f"| [#{item['number']}]({item['html_url']}) "
-                    f"| {kind} | {item['title']} | {', '.join(label_strs)} |"
-                )
-
-        if low_conf_labels:
-            lines.append("")
-            lines.append("<details>")
-            lines.append(f"<summary>Low-confidence suggestions ({len(low_conf_labels)} items)</summary>")
-            lines.append("")
-            lines.append("| # | Type | Title | Suggested Label |")
-            lines.append("|---|------|-------|--------------------|")
-            for idx, sugs in low_conf_labels:
-                item = items[idx]
-                kind = "PR" if item["is_pr"] else "Issue"
-                label_strs = [f"`{name}` ({score:.2f})" for name, score in sugs]
-                lines.append(
-                    f"| [#{item['number']}]({item['html_url']}) "
-                    f"| {kind} | {item['title']} | {', '.join(label_strs)} |"
-                )
-            lines.append("")
-            lines.append("</details>")
-
-        if not high_conf_labels and not low_conf_labels:
-            lines.append("No unlabeled items need suggestions.")
-
-    lines.extend([
-        "",
-        "### Summary",
-        "",
-        f"- {len(outlier_results)} outliers flagged for review",
-        f"- {len(duplicate_pairs)} duplicate pairs found",
-        f"- {len(items)} items analyzed in total",
-    ])
-
-    if label_suggestions is not None:
-        lines.append(f"- {suggested_count} items suggested for labeling")
-
-    lines.extend([
-        "",
-        "---",
-        f"*Generated by [triage-sweep](https://github.com/{repo}/actions) — no LLM was used.*",
-    ])
-
-    return "\n".join(lines)
-
-
-def create_report_issue(report_body: str) -> None:
-    """Create a GitHub issue with the triage report.
-
-    Posts to the issues API with the triage-report label.
-    Raises SystemExit on non-201 response.
-    """
-    token = os.environ["GITHUB_TOKEN"]
-    repo = os.environ["GITHUB_REPOSITORY"]
-    url = f"https://api.github.com/repos/{repo}/issues"
-
-    today = datetime.now(timezone.utc).strftime("%Y-%m-%d")
-    payload = json.dumps({
-        "title": f"Triage Sweep Report — {today}",
-        "body": report_body,
-        "labels": [REPORT_LABEL],
-    }).encode("utf-8")
-
-    req = urllib.request.Request(url, data=payload, method="POST")
-    req.add_header("Accept", "application/vnd.github+json")
-    req.add_header("Authorization", f"Bearer {token}")
-    req.add_header("X-GitHub-Api-Version", "2022-11-28")
-    req.add_header("Content-Type", "application/json")
-
-    try:
-        with urllib.request.urlopen(req, timeout=30) as resp:
-            resp_body = resp.read().decode("utf-8")
-            if resp.status != 201:
-                print(f"::error::Failed to create issue: {resp.status} {resp_body}")
-                sys.exit(1)
-            result = json.loads(resp_body)
-            print(f"Created issue: {result.get('html_url', 'unknown')}")
-    except urllib.error.HTTPError as e:
-        body = e.read().decode("utf-8", errors="replace")
-        print(f"::error::Failed to create issue: {e.code} {body}")
-        sys.exit(1)
-
-
-def write_report(report: str) -> None:
-    """Write the report to the file system for the summary step."""
-    with open(REPORT_FILE, "w", encoding="utf-8") as f:
-        f.write(report)
-
-
-def main() -> None:
-    """Orchestrate the full triage sweep."""
-    # 1. Validate environment
-    for var in ("GITHUB_TOKEN", "GITHUB_REPOSITORY"):
-        if not os.environ.get(var):
-            print(f"::error::Missing required environment variable: {var}")
-            sys.exit(1)
-
-    # 2. Fetch all open issues + PRs
-    items = fetch_all_open_items()
-    print(f"Fetched {len(items)} open items")
-
-    if len(items) == 0:
-        report = "## Triage Sweep Report\n\nNo open issues or PRs found."
-        write_report(report)
-        print("No items to analyze.")
-        return
-
-    # 3. Extract texts for embedding
-    texts: list[str] = [item["text"] for item in items]
-
-    # 4. Embed all texts (returns numpy float32 array of shape [n, 384])
-    embeddings = embed_texts(texts)
-
-    # 5. L2-normalize
-    embeddings = normalize_rows(embeddings)
-
-    # 6. Outlier detection (Mahalanobis via EllipticEnvelope)
-    outlier_results: list[tuple[int, float]] = []
-    if len(items) >= MIN_SAMPLES_FOR_OUTLIER_DETECTION:
-        reduced = reduce_dimensions(embeddings, PCA_MAX_COMPONENTS)
-        outlier_results = detect_outliers(
-            reduced,
-            contamination=CONTAMINATION,
-            iqr_multiplier=IQR_MULTIPLIER,
-            max_outlier_pct=MAX_OUTLIER_PCT,
-        )
-    else:
-        print(
-            f"Skipping outlier detection: {len(items)} items < "
-            f"{MIN_SAMPLES_FOR_OUTLIER_DETECTION} minimum"
-        )
-
-    # 7. Duplicate detection (pairwise cosine similarity)
-    duplicate_pairs = find_duplicate_pairs(embeddings, COSINE_THRESHOLD)
-
-    # 8. Label suggestion via embedding similarity
-    label_suggestions: list[list[tuple[str, float]]] | None = None
-    repo_labels = fetch_repo_labels()
-    if repo_labels:
-        label_texts = [lbl["text"] for lbl in repo_labels]
-        label_names = [lbl["name"] for lbl in repo_labels]
-        label_embeddings = embed_texts(label_texts)
-        label_embeddings = normalize_rows(label_embeddings)
-        label_suggestions = suggest_labels(embeddings, label_embeddings, label_names)
-        print(f"Computed label suggestions against {len(repo_labels)} repo labels")
-
-        # NOTE: Auto-labeling is disabled. The report shows suggestions for
-        # human review. To re-enable, uncomment the block below.
-        #
-        # # Apply top label to unlabeled items (unless dry run)
-        # # Skip outliers — flagged items shouldn't get categorized
-        # outlier_set = {idx for idx, _ in outlier_results}
-        # if not DRY_RUN:
-        #     applied_count = 0
-        #     for i, sugs in enumerate(label_suggestions):
-        #         if sugs and not items[i]["labels"] and i not in outlier_set:
-        #             # Apply only the top-1 label (highest confidence)
-        #             apply_labels_to_item(items[i]["number"], [sugs[0][0]])
-        #             applied_count += 1
-        #     print(f"Applied labels to {applied_count} unlabeled items")
-    else:
-        print("No repo labels found — skipping label suggestions")
-
-    # 9. Generate report
-    report = generate_report(items, outlier_results, duplicate_pairs, label_suggestions)
-
-    # 10. Write report to file (for summary step)
-    write_report(report)
-
-    # 11. Create report issue (unless dry run)
-    if DRY_RUN:
-        print("Dry run — skipping issue creation and label application.")
-        print(report)
-    else:
-        create_report_issue(report)
-        print("Report issue created.")
-
-
-if __name__ == "__main__":
-    main()

.github/scripts/triage/test_embedding_utils.py

@@ -1,468 +0,0 @@
-"""Tests for embedding_utils.py — all embedding model calls are mocked."""
-from __future__ import annotations
-
-import sys
-from unittest.mock import patch, MagicMock
-import numpy as np
-import pytest
-
-# Mock fastembed before importing the module under test (persistent)
-if "fastembed" not in sys.modules:
-    sys.modules["fastembed"] = MagicMock()
-
-from embedding_utils import (
-    embed_texts,
-    normalize_rows,
-    reduce_dimensions,
-    detect_outliers,
-    find_duplicate_pairs,
-    suggest_labels,
-    EMBEDDING_DIM,
-    EMBEDDING_MODEL,
-    EMBEDDING_BATCH_SIZE,
-    LABEL_Z_THRESHOLD,
-    LABEL_Z_MARGIN,
-    LABEL_Z_STD_FLOOR,
-    MIN_RAW_SIMILARITY,
-    MAX_LABELS_PER_ITEM,
-)
-
-
-class TestEmbedTexts:
-    """Tests for the embed_texts function."""
-
-    def test_empty_list_returns_empty_array(self):
-        result = embed_texts([])
-        assert result.shape == (0, EMBEDDING_DIM)
-        assert result.dtype == np.float32
-
-    @patch("embedding_utils.TextEmbedding")
-    def test_single_text(self, mock_cls):
-        mock_model = MagicMock()
-        mock_cls.return_value = mock_model
-        vec = np.random.randn(EMBEDDING_DIM).astype(np.float32)
-        mock_model.embed.return_value = iter([vec])
-
-        result = embed_texts(["hello world"])
-
-        mock_cls.assert_called_once_with(model_name=EMBEDDING_MODEL)
-        mock_model.embed.assert_called_once_with(
-            ["hello world"], batch_size=EMBEDDING_BATCH_SIZE
-        )
-        assert result.shape == (1, EMBEDDING_DIM)
-        assert result.dtype == np.float32
-        np.testing.assert_array_almost_equal(result[0], vec)
-
-    @patch("embedding_utils.TextEmbedding")
-    def test_multiple_texts(self, mock_cls):
-        mock_model = MagicMock()
-        mock_cls.return_value = mock_model
-        vecs = [
-            np.random.randn(EMBEDDING_DIM).astype(np.float32)
-            for _ in range(5)
-        ]
-        mock_model.embed.return_value = iter(vecs)
-
-        result = embed_texts(["a", "b", "c", "d", "e"])
-        assert result.shape == (5, EMBEDDING_DIM)
-        assert result.dtype == np.float32
-
-
-class TestNormalizeRows:
-    """Tests for L2 row normalization."""
-
-    def test_empty_matrix(self):
-        m = np.empty((0, 10), dtype=np.float32)
-        result = normalize_rows(m)
-        assert result.shape == (0, 10)
-
-    def test_single_row(self):
-        m = np.array([[3.0, 4.0]], dtype=np.float32)
-        result = normalize_rows(m)
-        # Norm should be ~1.0
-        norm = np.linalg.norm(result[0])
-        assert abs(norm - 1.0) < 1e-5
-
-    def test_multiple_rows(self):
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((10, 50)).astype(np.float32)
-        result = normalize_rows(m)
-        norms = np.linalg.norm(result, axis=1)
-        np.testing.assert_allclose(norms, 1.0, atol=1e-5)
-
-    def test_zero_row_stays_near_zero(self):
-        m = np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]], dtype=np.float32)
-        result = normalize_rows(m)
-        # Zero row divided by eps -> very small values
-        assert np.linalg.norm(result[0]) < 1e-3
-        # Non-zero row should be unit norm
-        assert abs(np.linalg.norm(result[1]) - 1.0) < 1e-5
-
-    def test_preserves_direction(self):
-        m = np.array([[2.0, 0.0], [0.0, 3.0]], dtype=np.float32)
-        result = normalize_rows(m)
-        np.testing.assert_allclose(result[0], [1.0, 0.0], atol=1e-5)
-        np.testing.assert_allclose(result[1], [0.0, 1.0], atol=1e-5)
-
-
-class TestReduceDimensions:
-    """Tests for PCA dimensionality reduction."""
-
-    def test_single_sample_returns_unchanged(self):
-        m = np.random.randn(1, 50).astype(np.float32)
-        result = reduce_dimensions(m, 10)
-        np.testing.assert_array_equal(result, m)
-
-    def test_reduces_dimensions(self):
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((100, 50)).astype(np.float32)
-        result = reduce_dimensions(m, 10)
-        assert result.shape == (100, 10)
-        assert result.dtype == np.float32
-
-    def test_caps_at_n_minus_1(self):
-        rng = np.random.default_rng(42)
-        # 5 samples, 20 features -> max components = 4 (n-1)
-        m = rng.standard_normal((5, 20)).astype(np.float32)
-        result = reduce_dimensions(m, 50)
-        assert result.shape == (5, 4)
-
-    def test_caps_at_d(self):
-        rng = np.random.default_rng(42)
-        # 100 samples, 3 features -> max components = 3
-        m = rng.standard_normal((100, 3)).astype(np.float32)
-        result = reduce_dimensions(m, 50)
-        assert result.shape == (100, 3)
-
-    def test_max_components_respected(self):
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((50, 30)).astype(np.float32)
-        result = reduce_dimensions(m, 5)
-        assert result.shape[1] == 5
-
-
-class TestDetectOutliers:
-    """Tests for IQR-based outlier detection."""
-
-    def test_single_sample_returns_empty(self):
-        m = np.random.randn(1, 5).astype(np.float32)
-        result = detect_outliers(m)
-        assert result == []
-
-    def test_empty_returns_empty(self):
-        # n < 2 case
-        m = np.empty((0, 5), dtype=np.float32)
-        result = detect_outliers(m)
-        assert result == []
-
-    def test_finds_outliers_in_synthetic_data(self):
-        rng = np.random.default_rng(42)
-        # Create a tight cluster with one obvious outlier
-        cluster = rng.standard_normal((50, 3)).astype(np.float32) * 0.1
-        outlier = np.array([[100.0, 100.0, 100.0]], dtype=np.float32)
-        m = np.vstack([cluster, outlier])
-        result = detect_outliers(m)
-        # The outlier (index 50) should be detected
-        outlier_indices = [idx for idx, _ in result]
-        assert 50 in outlier_indices
-
-    def test_returns_list_of_index_distance_tuples(self):
-        rng = np.random.default_rng(42)
-        # Tight cluster + outlier to guarantee at least one result
-        cluster = rng.standard_normal((20, 3)).astype(np.float32) * 0.1
-        far_point = np.array([[50.0, 50.0, 50.0]], dtype=np.float32)
-        m = np.vstack([cluster, far_point])
-        result = detect_outliers(m)
-        assert isinstance(result, list)
-        for item in result:
-            assert isinstance(item, tuple)
-            assert len(item) == 2
-            idx, dist = item
-            assert isinstance(idx, int)
-            assert isinstance(dist, float)
-            assert dist > 0
-
-    def test_iqr_cutoff_behavior(self):
-        """Lower IQR multiplier should flag more items than higher multiplier."""
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((100, 3)).astype(np.float32)
-        low = detect_outliers(m, iqr_multiplier=1.0, max_outlier_pct=0.5)
-        high = detect_outliers(m, iqr_multiplier=5.0, max_outlier_pct=0.5)
-        assert len(low) >= len(high)
-
-    def test_dimension_aware_no_mass_flagging(self):
-        """High-dimensional clean Gaussian data should not flag everything."""
-        rng = np.random.default_rng(42)
-        # 500 samples, 10 dims — well-conditioned for robust covariance
-        m = rng.standard_normal((500, 10)).astype(np.float32)
-        result = detect_outliers(m)
-        # With IQR-based cutoff on clean Gaussian data,
-        # only a small fraction should be flagged (well under 50%)
-        assert len(result) < 250
-
-    def test_contamination_parameter(self):
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((50, 3)).astype(np.float32)
-        # Should not raise with different contamination values
-        result = detect_outliers(m, contamination=0.05)
-        assert isinstance(result, list)
-
-    def test_max_outlier_pct_hard_cap(self):
-        """The hard cap should limit outlier count to max_outlier_pct * n."""
-        rng = np.random.default_rng(42)
-        # Create data with many potential outliers (bimodal)
-        cluster = rng.standard_normal((80, 3)).astype(np.float32) * 0.1
-        outliers = rng.standard_normal((20, 3)).astype(np.float32) * 50.0
-        m = np.vstack([cluster, outliers])
-        # Very low IQR multiplier to flag a lot, but cap at 5%
-        result = detect_outliers(m, iqr_multiplier=0.5, max_outlier_pct=0.05)
-        max_allowed = max(1, int(0.05 * 100))  # 5
-        assert len(result) <= max_allowed
-
-    def test_hard_cap_keeps_most_extreme(self):
-        """When capped, the most extreme items (highest distance) should be kept."""
-        rng = np.random.default_rng(42)
-        cluster = rng.standard_normal((90, 3)).astype(np.float32) * 0.1
-        # Create outliers with increasing extremity
-        outliers = np.array([
-            [10.0, 10.0, 10.0],
-            [20.0, 20.0, 20.0],
-            [50.0, 50.0, 50.0],
-        ], dtype=np.float32)
-        m = np.vstack([cluster, outliers])
-        # Cap at ~1 item (0.01 * 93 = 0, but min is 1)
-        result = detect_outliers(m, iqr_multiplier=0.5, max_outlier_pct=0.02)
-        if len(result) > 0:
-            # The most extreme (index 92, distance for [50,50,50]) should be kept
-            indices = [idx for idx, _ in result]
-            assert 92 in indices
-
-    def test_cutoff_attribute(self):
-        """Returned result should carry a cutoff attribute."""
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((50, 3)).astype(np.float32)
-        result = detect_outliers(m)
-        assert hasattr(result, "cutoff")
-        assert isinstance(result.cutoff, float)
-        assert result.cutoff > 0
-
-
-class TestFindDuplicatePairs:
-    """Tests for cosine similarity duplicate detection."""
-
-    def test_single_item_returns_empty(self):
-        m = np.random.randn(1, 10).astype(np.float32)
-        result = find_duplicate_pairs(m, 0.9)
-        assert result == []
-
-    def test_empty_returns_empty(self):
-        m = np.empty((0, 10), dtype=np.float32)
-        result = find_duplicate_pairs(m, 0.9)
-        assert result == []
-
-    def test_identical_vectors_detected(self):
-        vec = np.random.randn(10).astype(np.float32)
-        vec = vec / np.linalg.norm(vec)
-        m = np.vstack([vec, vec, np.random.randn(10).astype(np.float32)])
-        result = find_duplicate_pairs(m, 0.99)
-        # Items 0 and 1 are identical, should be found
-        assert any(i == 0 and j == 1 for i, j, _ in result)
-
-    def test_orthogonal_vectors_not_detected(self):
-        m = np.eye(5, dtype=np.float32)
-        result = find_duplicate_pairs(m, 0.5)
-        assert result == []
-
-    def test_returns_correct_format(self):
-        vec = np.random.randn(10).astype(np.float32)
-        vec = vec / np.linalg.norm(vec)
-        m = np.vstack([vec, vec])
-        result = find_duplicate_pairs(m, 0.5)
-        assert len(result) >= 1
-        for item in result:
-            assert len(item) == 3
-            i, j, sim = item
-            assert isinstance(i, int)
-            assert isinstance(j, int)
-            assert isinstance(sim, float)
-            assert i < j
-
-    def test_i_less_than_j(self):
-        rng = np.random.default_rng(42)
-        # Create some similar vectors
-        base = rng.standard_normal(10).astype(np.float32)
-        m = np.vstack([base + rng.standard_normal(10) * 0.01 for _ in range(5)])
-        result = find_duplicate_pairs(m, 0.5)
-        for i, j, _ in result:
-            assert i < j
-
-    def test_high_threshold_fewer_pairs(self):
-        rng = np.random.default_rng(42)
-        m = rng.standard_normal((10, 20)).astype(np.float32)
-        # Normalize for meaningful cosine similarities
-        norms = np.linalg.norm(m, axis=1, keepdims=True)
-        m = m / norms
-        low = find_duplicate_pairs(m, 0.3)
-        high = find_duplicate_pairs(m, 0.9)
-        assert len(low) >= len(high)
-
-
-class TestSuggestLabels:
-    """Tests for z-score normalized label suggestion."""
-
-    def test_empty_items_returns_empty_lists(self):
-        items = np.empty((0, 10), dtype=np.float32)
-        labels = np.random.randn(3, 10).astype(np.float32)
-        result = suggest_labels(items, labels, ["a", "b", "c"])
-        assert result == []
-
-    def test_empty_labels_returns_empty_per_item(self):
-        items = np.random.randn(5, 10).astype(np.float32)
-        labels = np.empty((0, 10), dtype=np.float32)
-        result = suggest_labels(items, labels, [])
-        assert len(result) == 5
-        assert all(s == [] for s in result)
-
-    def test_identical_embedding_gets_that_label(self):
-        """If an item embedding strongly matches one label, z-score should highlight it."""
-        # Create multiple items so z-score normalization is meaningful
-        rng = np.random.default_rng(42)
-        # 10 random items + 1 item that matches label "bug" exactly
-        random_items = rng.standard_normal((10, 3)).astype(np.float32)
-        bug_vec = np.array([[1.0, 0.0, 0.0]], dtype=np.float32)
-        items = np.vstack([random_items, bug_vec])
-        labels = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]], dtype=np.float32)
-        result = suggest_labels(
-            items, labels, ["bug", "feature", "docs"],
-            z_threshold=0.5, z_margin=0.0, min_raw_sim=0.1,
-        )
-        # The last item (matching bug_vec) should get "bug" as top suggestion
-        last_item_sugs = result[-1]
-        if last_item_sugs:
-            assert last_item_sugs[0][0] == "bug"
-
-    def test_z_score_suppresses_dominant_label(self):
-        """When all items are similar to one label, z-scores should be low
-        (none stands out) and that label should not be blindly suggested."""
-        # All items identical — z-score for every item on every label is 0
-        items = np.ones((10, 3), dtype=np.float32)
-        labels = np.array([[1.0, 1.0, 1.0], [0.0, 1.0, 0.0]], dtype=np.float32)
-        result = suggest_labels(
-            items, labels, ["catch-all", "specific"],
-            z_threshold=1.5, min_raw_sim=0.3,
-        )
-        # With identical items, std=0 -> z-scores are all 0 -> nothing passes z_threshold
-        for sugs in result:
-            assert sugs == []
-
-    def test_margin_gate_blocks_top1(self):
-        """Top-1 label must beat #2 by z_margin to be accepted as position 0."""
-        rng = np.random.default_rng(99)
-        # 20 items, each slightly different, 2 labels
-        items = rng.standard_normal((20, 5)).astype(np.float32)
-        # Two labels that are nearly identical -> margin gate should block top-1
-        labels = np.array([[1.0, 0.5, 0.0, 0.0, 0.0],
-                           [1.0, 0.5, 0.01, 0.0, 0.0]], dtype=np.float32)
-        result = suggest_labels(
-            items, labels, ["label-a", "label-b"],
-            z_threshold=0.0, z_margin=10.0, min_raw_sim=0.0, max_per_item=1,
-        )
-        # With a huge margin requirement and max_per_item=1, nothing should pass
-        # because the only candidate (top-1) is blocked by margin gate,
-        # and max_per_item=1 prevents falling through to position 2
-        for sugs in result:
-            assert sugs == []
-
-    def test_margin_gate_passes_when_clear_winner(self):
-        """When top-1 clearly beats #2, it should pass the margin gate."""
-        # Create items where one strongly matches label 0 vs label 1
-        items = np.array([
-            [1.0, 0.0, 0.0, 0.0, 0.0],   # strongly matches label-a
-            [0.0, 0.0, 0.0, 0.0, 1.0],   # matches neither well
-        ] * 5, dtype=np.float32)  # 10 items for stable z-scores
-        labels = np.array([
-            [1.0, 0.0, 0.0, 0.0, 0.0],   # label-a
-            [0.0, 1.0, 0.0, 0.0, 0.0],   # label-b (orthogonal)
-        ], dtype=np.float32)
-        result = suggest_labels(
-            items, labels, ["label-a", "label-b"],
-            z_threshold=0.5, z_margin=0.3, min_raw_sim=0.1,
-        )
-        # Items matching label-a should get it suggested (clear z-score advantage)
-        got_label_a = sum(1 for sugs in result if sugs and sugs[0][0] == "label-a")
-        assert got_label_a > 0
-
-    def test_min_raw_similarity_filter(self):
-        """Even with high z-score, low raw similarity should be filtered out."""
-        # Items are orthogonal to all labels -> raw similarity near 0
-        items = np.array([[1.0, 0.0, 0.0]], dtype=np.float32)
-        labels = np.array([[0.0, 0.0, 1.0]], dtype=np.float32)
-        result = suggest_labels(
-            items, labels, ["irrelevant"],
-            z_threshold=0.0, z_margin=0.0, min_raw_sim=0.9,
-        )
-        # Raw similarity is ~0, which is below min_raw_sim=0.9
-        assert result[0] == []
-
-    def test_max_per_item_respected(self):
-        """Even if many labels qualify, max_per_item caps the results."""
-        rng = np.random.default_rng(42)
-        # Create items with some variance so z-scores differentiate
-        items = rng.standard_normal((20, 10)).astype(np.float32)
-        base = items[0]
-        # All labels very similar to item 0
-        labels = np.array([base + rng.standard_normal(10) * 0.01 for _ in range(10)])
-        names = [f"label-{i}" for i in range(10)]
-        result = suggest_labels(
-            items, labels, names,
-            z_threshold=0.0, z_margin=0.0, min_raw_sim=0.0, max_per_item=2,
-        )
-        for sugs in result:
-            assert len(sugs) <= 2
-
-    def test_returns_raw_similarity_not_z_score(self):
-        """Returned scores should be raw cosine similarity, not z-scores."""
-        rng = np.random.default_rng(42)
-        items = rng.standard_normal((15, 5)).astype(np.float32)
-        labels = rng.standard_normal((3, 5)).astype(np.float32)
-        names = ["bug", "feature", "docs"]
-        result = suggest_labels(
-            items, labels, names,
-            z_threshold=0.0, z_margin=0.0, min_raw_sim=-1.0,
-        )
-        # Raw cosine similarity should be in [-1, 1] range
-        for sugs in result:
-            for name, score in sugs:
-                assert -1.0 <= score <= 1.0 + 1e-5
-                assert isinstance(name, str)
-                assert isinstance(score, float)
-
-    def test_returns_correct_format(self):
-        rng = np.random.default_rng(42)
-        items = rng.standard_normal((3, 10)).astype(np.float32)
-        labels = rng.standard_normal((5, 10)).astype(np.float32)
-        names = ["bug", "feature", "docs", "ci", "test"]
-        result = suggest_labels(
-            items, labels, names,
-            z_threshold=0.0, z_margin=0.0, min_raw_sim=-1.0,
-        )
-        assert len(result) == 3
-        for sugs in result:
-            for name, score in sugs:
-                assert isinstance(name, str)
-                assert isinstance(score, float)
-                assert name in names
-
-    def test_text_truncation_in_labels(self):
-        """Label names should be returned as-is even when very long."""
-        rng = np.random.default_rng(42)
-        items = rng.standard_normal((10, 5)).astype(np.float32)
-        long_name = "a" * 200
-        labels = rng.standard_normal((1, 5)).astype(np.float32)
-        result = suggest_labels(
-            items, labels, [long_name],
-            z_threshold=0.0, z_margin=0.0, min_raw_sim=-1.0,
-        )
-        for sugs in result:
-            if sugs:
-                assert sugs[0][0] == long_name

.github/scripts/triage/test_sweep.py

@@ -1,873 +0,0 @@
-"""Tests for sweep.py — all external calls (API, embedding) are mocked."""
-from __future__ import annotations
-
-import json
-import os
-import sys
-from io import BytesIO
-from unittest.mock import patch, MagicMock, mock_open
-from urllib.error import HTTPError
-
-import numpy as np
-import pytest
-
-# Mock fastembed before importing sweep (which imports embedding_utils)
-sys.modules["fastembed"] = MagicMock()
-
-# Set required env vars before importing sweep (module-level constants read env)
-os.environ.setdefault("GITHUB_TOKEN", "test-token")
-os.environ.setdefault("GITHUB_REPOSITORY", "owner/repo")
-
-from sweep import (
-    github_api_get,
-    fetch_all_open_items,
-    fetch_repo_labels,
-    apply_labels_to_item,
-    generate_report,
-    create_report_issue,
-    write_report,
-    main,
-    TriageItem,
-    RepoLabel,
-    REPORT_FILE,
-    REPORT_LABEL,
-    API_PAGE_SIZE,
-    MIN_SAMPLES_FOR_OUTLIER_DETECTION,
-    PCA_MAX_COMPONENTS,
-    MAX_EMBED_CHARS,
-    IQR_MULTIPLIER,
-    MAX_OUTLIER_PCT,
-    _item_age,
-    _suggested_action,
-)
-
-
-def _make_api_issue(number: int, title: str = "Test issue", is_pr: bool = False,
-                    body: str = "Issue body", labels: list[str] | None = None,
-                    created_at: str = "2026-03-21T00:00:00Z") -> dict:
-    """Helper to build a mock GitHub API issue response object."""
-    result: dict = {
-        "number": number,
-        "title": title,
-        "html_url": f"https://github.com/owner/repo/issues/{number}",
-        "body": body,
-        "created_at": created_at,
-        "labels": [{"name": lbl} for lbl in (labels or [])],
-    }
-    if is_pr:
-        result["pull_request"] = {"url": "..."}
-    return result
-
-
-class TestGithubApiGet:
-    """Tests for the github_api_get function."""
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_successful_request(self, mock_urlopen):
-        mock_resp = MagicMock()
-        mock_resp.read.return_value = json.dumps([{"id": 1}]).encode()
-        mock_resp.__enter__ = lambda s: s
-        mock_resp.__exit__ = MagicMock(return_value=False)
-        mock_urlopen.return_value = mock_resp
-
-        result = github_api_get("/issues?state=open")
-        assert result == [{"id": 1}]
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_http_error_exits(self, mock_urlopen):
-        error = HTTPError(
-            url="https://api.github.com/repos/owner/repo/issues",
-            code=403,
-            msg="Forbidden",
-            hdrs=None,  # type: ignore[arg-type]
-            fp=BytesIO(b'{"message": "rate limited"}'),
-        )
-        mock_urlopen.side_effect = error
-
-        with pytest.raises(SystemExit) as exc_info:
-            github_api_get("/issues")
-        assert exc_info.value.code == 1
-
-
-class TestConstants:
-    """Tests for module-level constants."""
-
-    def test_min_samples_is_at_least_3x_pca_max(self):
-        """MIN_SAMPLES must be >= 3 * PCA_MAX_COMPONENTS for reliable covariance."""
-        assert MIN_SAMPLES_FOR_OUTLIER_DETECTION >= 3 * PCA_MAX_COMPONENTS
-
-    def test_min_samples_is_100(self):
-        assert MIN_SAMPLES_FOR_OUTLIER_DETECTION == 100
-
-    def test_pca_max_components_is_20(self):
-        assert PCA_MAX_COMPONENTS == 20
-
-    def test_iqr_multiplier_default(self):
-        assert IQR_MULTIPLIER == 3.0
-
-    def test_max_outlier_pct_default(self):
-        assert MAX_OUTLIER_PCT == 0.05
-
-
-class TestFetchAllOpenItems:
-    """Tests for fetch_all_open_items."""
-
-    @patch("sweep.github_api_get")
-    def test_empty_repo(self, mock_get):
-        mock_get.return_value = []
-        items = fetch_all_open_items()
-        assert items == []
-
-    @patch("sweep.github_api_get")
-    def test_single_page(self, mock_get):
-        mock_get.return_value = [
-            _make_api_issue(1, "Bug report"),
-            _make_api_issue(2, "Feature request", is_pr=True),
-        ]
-        items = fetch_all_open_items()
-        assert len(items) == 2
-        assert items[0]["number"] == 1
-        assert items[0]["is_pr"] is False
-        assert items[1]["is_pr"] is True
-
-    @patch("sweep.github_api_get")
-    def test_text_field_constructed(self, mock_get):
-        mock_get.return_value = [
-            _make_api_issue(1, "My Title", body="My Body"),
-        ]
-        items = fetch_all_open_items()
-        assert items[0]["text"] == "My Title\n\nMy Body"
-
-    @patch("sweep.github_api_get")
-    def test_long_body_truncated(self, mock_get):
-        """Bodies exceeding MAX_EMBED_CHARS are truncated to fit the token window."""
-        long_body = "x" * (MAX_EMBED_CHARS + 500)
-        mock_get.return_value = [
-            _make_api_issue(1, "Title", body=long_body),
-        ]
-        items = fetch_all_open_items()
-        assert len(items[0]["text"]) == MAX_EMBED_CHARS
-
-    @patch("sweep.github_api_get")
-    def test_short_body_not_truncated(self, mock_get):
-        """Bodies under the limit are left intact."""
-        mock_get.return_value = [
-            _make_api_issue(1, "Title", body="Short body"),
-        ]
-        items = fetch_all_open_items()
-        assert items[0]["text"] == "Title\n\nShort body"
-
-    @patch("sweep.github_api_get")
-    def test_null_body_handled(self, mock_get):
-        issue = _make_api_issue(1, "No body")
-        issue["body"] = None
-        mock_get.return_value = [issue]
-        items = fetch_all_open_items()
-        assert items[0]["text"] == "No body\n\n"
-
-    @patch("sweep.github_api_get")
-    def test_labels_extracted(self, mock_get):
-        mock_get.return_value = [
-            _make_api_issue(1, "Labeled", labels=["bug", "high-priority"]),
-        ]
-        items = fetch_all_open_items()
-        assert items[0]["labels"] == ["bug", "high-priority"]
-
-    @patch("sweep.MAX_ITEMS", 3)
-    @patch("sweep.github_api_get")
-    def test_max_items_cap(self, mock_get):
-        mock_get.return_value = [_make_api_issue(i) for i in range(100)]
-        items = fetch_all_open_items()
-        assert len(items) == 3
-
-    @patch("sweep.API_PAGE_SIZE", 2)
-    @patch("sweep.github_api_get")
-    def test_pagination(self, mock_get):
-        # First page: 2 items (full page), second page: 1 item (partial -> stop)
-        mock_get.side_effect = [
-            [_make_api_issue(1), _make_api_issue(2)],
-            [_make_api_issue(3)],
-        ]
-        items = fetch_all_open_items()
-        assert len(items) == 3
-        assert mock_get.call_count == 2
-
-
-class TestItemAge:
-    """Tests for _item_age helper."""
-
-    def test_recent_item(self):
-        from datetime import datetime, timezone, timedelta
-        recent = (datetime.now(timezone.utc) - timedelta(hours=12)).isoformat()
-        assert _item_age(recent) == "<1d"
-
-    def test_days_old(self):
-        from datetime import datetime, timezone, timedelta
-        old = (datetime.now(timezone.utc) - timedelta(days=15)).isoformat()
-        assert _item_age(old) == "15d"
-
-    def test_months_old(self):
-        from datetime import datetime, timezone, timedelta
-        old = (datetime.now(timezone.utc) - timedelta(days=90)).isoformat()
-        assert _item_age(old) == "3mo"
-
-    def test_years_old(self):
-        from datetime import datetime, timezone, timedelta
-        old = (datetime.now(timezone.utc) - timedelta(days=400)).isoformat()
-        assert _item_age(old) == "1y"
-
-    def test_invalid_date(self):
-        assert _item_age("not-a-date") == "?"
-
-
-class TestSuggestedAction:
-    """Tests for _suggested_action helper."""
-
-    def test_both_issues_close_newer(self):
-        a = TriageItem(
-            number=1, title="A", html_url="u", is_pr=False, labels=[],
-            created_at="2026-01-01T00:00:00Z", text="t",
-        )
-        b = TriageItem(
-            number=2, title="B", html_url="u", is_pr=False, labels=[],
-            created_at="2026-02-01T00:00:00Z", text="t",
-        )
-        result = _suggested_action(a, b)
-        assert "Close #2 as duplicate" in result
-
-    def test_both_prs_review(self):
-        a = TriageItem(
-            number=1, title="A", html_url="u", is_pr=True, labels=[],
-            created_at="2026-01-01T00:00:00Z", text="t",
-        )
-        b = TriageItem(
-            number=2, title="B", html_url="u", is_pr=True, labels=[],
-            created_at="2026-01-01T00:00:00Z", text="t",
-        )
-        assert _suggested_action(a, b) == "Review for overlap"
-
-    def test_issue_pr_link(self):
-        a = TriageItem(
-            number=1, title="A", html_url="u", is_pr=False, labels=[],
-            created_at="2026-01-01T00:00:00Z", text="t",
-        )
-        b = TriageItem(
-            number=2, title="B", html_url="u", is_pr=True, labels=[],
-            created_at="2026-01-01T00:00:00Z", text="t",
-        )
-        assert _suggested_action(a, b) == "Link PR to issue"
-
-
-class TestGenerateReport:
-    """Tests for the markdown report generator."""
-
-    def test_no_findings(self):
-        items = [
-            TriageItem(
-                number=1, title="Test", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="Test",
-            ),
-        ]
-        report = generate_report(items, [], [])
-        assert "## Triage Sweep Report" in report
-        assert "Items analyzed:** 1" in report
-        assert "None found." in report
-        assert "0 outliers flagged" in report
-        assert "0 duplicate pairs found" in report
-
-    def test_health_summary_table(self):
-        items = [
-            TriageItem(
-                number=1, title="Test", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="Test",
-            ),
-        ]
-        report = generate_report(items, [], [])
-        assert "### Health Summary" in report
-        assert "| Metric | Value |" in report
-        assert "| Items analyzed | 1 |" in report
-
-    def test_iqr_multiplier_in_thresholds(self):
-        """Report should show IQR multiplier, not percentile."""
-        items = [
-            TriageItem(
-                number=1, title="Test", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="Test",
-            ),
-        ]
-        report = generate_report(items, [], [])
-        assert "IQR multiplier" in report
-        assert "percentile" not in report.lower().split("thresholds")[0]  # not in thresholds line
-
-    def test_with_outliers_shows_distance_and_age(self):
-        items = [
-            TriageItem(
-                number=10, title="Spam Issue", html_url="https://example.com/10",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="spam",
-            ),
-            TriageItem(
-                number=20, title="Good Issue", html_url="https://example.com/20",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="good",
-            ),
-        ]
-        report = generate_report(items, [(0, 12.34)], [])
-        assert "#10" in report
-        assert "Spam Issue" in report
-        assert "12.34" in report
-        assert "1 outliers flagged" in report
-        # Age column should be present
-        assert "| Age |" in report
-
-    def test_outlier_borderline_in_details(self):
-        """Borderline outliers should be in a <details> section."""
-        from embedding_utils import _OutlierResult
-        items = [
-            TriageItem(
-                number=10, title="Borderline", html_url="https://example.com/10",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="spam",
-            ),
-        ]
-        # Create outlier results with cutoff=10.0, distance=12.0 (< 2*cutoff=20)
-        outlier_results = _OutlierResult([(0, 12.0)])
-        outlier_results.cutoff = 10.0
-        report = generate_report(items, outlier_results, [])
-        assert "<details>" in report
-        assert "Borderline" in report
-
-    def test_outlier_high_confidence(self):
-        """Items with distance > 2x cutoff should be in high confidence section."""
-        from embedding_utils import _OutlierResult
-        items = [
-            TriageItem(
-                number=10, title="Definite Spam", html_url="https://example.com/10",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="spam",
-            ),
-        ]
-        outlier_results = _OutlierResult([(0, 25.0)])
-        outlier_results.cutoff = 10.0
-        report = generate_report(items, outlier_results, [])
-        assert "High Confidence" in report
-
-    def test_with_duplicates_suggested_action(self):
-        items = [
-            TriageItem(
-                number=1, title="First", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="a",
-            ),
-            TriageItem(
-                number=2, title="Second", html_url="https://example.com/2",
-                is_pr=True, labels=[], created_at="2026-02-01T00:00:00Z", text="b",
-            ),
-        ]
-        report = generate_report(items, [], [(0, 1, 0.954)])
-        assert "#1" in report
-        assert "#2" in report
-        assert "0.954" in report
-        assert "1 duplicate pairs found" in report
-        assert "Suggested Action" in report
-        assert "Link PR to issue" in report
-
-    def test_duplicate_both_issues_close_newer(self):
-        items = [
-            TriageItem(
-                number=1, title="First", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="a",
-            ),
-            TriageItem(
-                number=2, title="Second", html_url="https://example.com/2",
-                is_pr=False, labels=[], created_at="2026-02-01T00:00:00Z", text="b",
-            ),
-        ]
-        report = generate_report(items, [], [(0, 1, 0.95)])
-        assert "Close #2 as duplicate" in report
-
-    def test_duplicate_both_prs_review(self):
-        items = [
-            TriageItem(
-                number=1, title="PR A", html_url="https://example.com/1",
-                is_pr=True, labels=[], created_at="2026-01-01T00:00:00Z", text="a",
-            ),
-            TriageItem(
-                number=2, title="PR B", html_url="https://example.com/2",
-                is_pr=True, labels=[], created_at="2026-01-01T00:00:00Z", text="b",
-            ),
-        ]
-        report = generate_report(items, [], [(0, 1, 0.95)])
-        assert "Review for overlap" in report
-
-    def test_pr_type_label(self):
-        items = [
-            TriageItem(
-                number=5, title="PR Title", html_url="https://example.com/5",
-                is_pr=True, labels=[], created_at="2026-01-01T00:00:00Z", text="pr",
-            ),
-        ]
-        report = generate_report(items, [(0, 8.5)], [])
-        assert "| PR |" in report
-
-    def test_footer_present(self):
-        items = [
-            TriageItem(
-                number=1, title="T", html_url="u",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="t",
-            ),
-        ]
-        report = generate_report(items, [], [])
-        assert "no LLM was used" in report
-
-
-class TestCreateReportIssue:
-    """Tests for creating the report GitHub issue."""
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_successful_creation(self, mock_urlopen):
-        mock_resp = MagicMock()
-        mock_resp.status = 201
-        mock_resp.read.return_value = json.dumps({
-            "html_url": "https://github.com/owner/repo/issues/99",
-        }).encode()
-        mock_resp.__enter__ = lambda s: s
-        mock_resp.__exit__ = MagicMock(return_value=False)
-        mock_urlopen.return_value = mock_resp
-
-        # Should not raise
-        create_report_issue("# Test Report")
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_http_error_exits(self, mock_urlopen):
-        error = HTTPError(
-            url="https://api.github.com/repos/owner/repo/issues",
-            code=422,
-            msg="Unprocessable",
-            hdrs=None,  # type: ignore[arg-type]
-            fp=BytesIO(b'{"message": "validation failed"}'),
-        )
-        mock_urlopen.side_effect = error
-
-        with pytest.raises(SystemExit) as exc_info:
-            create_report_issue("# Test Report")
-        assert exc_info.value.code == 1
-
-
-class TestWriteReport:
-    """Tests for the write_report helper."""
-
-    @patch("builtins.open", mock_open())
-    def test_writes_to_file(self):
-        write_report("# Report Content")
-        from builtins import open as builtin_open  # noqa
-        # Verify open was called with the right path
-        from unittest.mock import call
-        open_mock = open  # The patched version
-        open_mock.assert_called_once_with(REPORT_FILE, "w", encoding="utf-8")  # type: ignore[attr-defined]
-        open_mock().write.assert_called_once_with("# Report Content")  # type: ignore[attr-defined]
-
-
-class TestFetchRepoLabels:
-    """Tests for fetch_repo_labels."""
-
-    @patch("sweep.github_api_get")
-    def test_fetches_and_constructs_labels(self, mock_get):
-        mock_get.return_value = [
-            {"name": "bug", "description": "Something isn't working"},
-            {"name": "enhancement", "description": "New feature or request"},
-            {"name": "docs", "description": ""},
-        ]
-        labels = fetch_repo_labels()
-        assert len(labels) == 3
-        assert labels[0]["name"] == "bug"
-        assert labels[0]["text"] == "bug: Something isn't working"
-        assert labels[2]["text"] == "docs"  # no description, just name
-
-    @patch("sweep.github_api_get")
-    def test_empty_repo_labels(self, mock_get):
-        mock_get.return_value = []
-        labels = fetch_repo_labels()
-        assert labels == []
-
-    @patch("sweep.github_api_get")
-    def test_null_description_handled(self, mock_get):
-        mock_get.return_value = [
-            {"name": "wontfix", "description": None},
-        ]
-        labels = fetch_repo_labels()
-        assert labels[0]["text"] == "wontfix"
-
-    @patch("sweep.API_PAGE_SIZE", 2)
-    @patch("sweep.github_api_get")
-    def test_label_pagination(self, mock_get):
-        """Repos with more labels than one page should fetch all pages."""
-        mock_get.side_effect = [
-            # First page: full (2 items = API_PAGE_SIZE)
-            [
-                {"name": "bug", "description": "Broken"},
-                {"name": "feature", "description": "New"},
-            ],
-            # Second page: partial (1 item < API_PAGE_SIZE) -> stop
-            [
-                {"name": "docs", "description": "Documentation"},
-            ],
-        ]
-        labels = fetch_repo_labels()
-        assert len(labels) == 3
-        assert mock_get.call_count == 2
-        assert labels[0]["name"] == "bug"
-        assert labels[2]["name"] == "docs"
-
-
-class TestApplyLabelsToItem:
-    """Tests for apply_labels_to_item."""
-
-    def test_empty_labels_skips(self):
-        # Should not make any API call
-        apply_labels_to_item(1, [])
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_successful_label_application(self, mock_urlopen):
-        mock_resp = MagicMock()
-        mock_resp.read.return_value = b'[{"name": "bug"}]'
-        mock_resp.__enter__ = lambda s: s
-        mock_resp.__exit__ = MagicMock(return_value=False)
-        mock_urlopen.return_value = mock_resp
-
-        # Should not raise
-        apply_labels_to_item(42, ["bug", "enhancement"])
-
-    @patch("sweep.urllib.request.urlopen")
-    def test_http_error_is_non_fatal(self, mock_urlopen):
-        error = HTTPError(
-            url="https://api.github.com/repos/owner/repo/issues/1/labels",
-            code=404,
-            msg="Not Found",
-            hdrs=None,  # type: ignore[arg-type]
-            fp=BytesIO(b'{"message": "not found"}'),
-        )
-        mock_urlopen.side_effect = error
-
-        # Should NOT raise — labeling failures are warnings, not fatal
-        apply_labels_to_item(1, ["bug"])
-
-
-class TestGenerateReportWithLabels:
-    """Tests for label suggestions in the report."""
-
-    def test_report_includes_label_section_high_confidence(self):
-        """High-confidence label (raw_sim >= 0.5) should appear in main table."""
-        items = [
-            TriageItem(
-                number=1, title="Fix crash", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="crash",
-            ),
-        ]
-        suggestions = [[("bug", 0.85)]]
-        report = generate_report(items, [], [], label_suggestions=suggestions)
-        assert "Suggested Labels" in report
-        assert "`bug` (0.85)" in report
-        assert "1 items suggested for labeling" in report
-
-    def test_report_low_confidence_in_details(self):
-        """Low-confidence label (raw_sim < 0.5) should be in <details> section."""
-        items = [
-            TriageItem(
-                number=1, title="Something", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="something",
-            ),
-        ]
-        suggestions = [[("maybe-bug", 0.35)]]
-        report = generate_report(items, [], [], label_suggestions=suggestions)
-        assert "Low-confidence suggestions" in report
-        assert "<details>" in report
-        assert "`maybe-bug` (0.35)" in report
-
-    def test_report_skips_already_labeled_items(self):
-        items = [
-            TriageItem(
-                number=1, title="Already labeled", html_url="https://example.com/1",
-                is_pr=False, labels=["bug"], created_at="2026-01-01T00:00:00Z", text="bug",
-            ),
-        ]
-        suggestions = [[("bug", 0.95)]]
-        report = generate_report(items, [], [], label_suggestions=suggestions)
-        assert "0 items suggested for labeling" in report
-        assert "No unlabeled items" in report
-
-    def test_report_excludes_outliers_from_suggestions(self):
-        items = [
-            TriageItem(
-                number=1, title="Spam garbage", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="spam",
-            ),
-            TriageItem(
-                number=2, title="Real bug", html_url="https://example.com/2",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="bug",
-            ),
-        ]
-        suggestions = [[("bug", 0.85)], [("bug", 0.90)]]
-        # Item 0 is an outlier (with distance) — should be excluded from label suggestions
-        report = generate_report(items, [(0, 15.2)], [], label_suggestions=suggestions)
-        assert "1 unlabeled items" in report  # only item 2
-        assert "#2" in report
-        # Item 0 (outlier) should NOT be in the suggestions table
-        assert "Spam garbage" not in report.split("Suggested Labels")[1]
-
-    def test_report_without_label_suggestions(self):
-        items = [
-            TriageItem(
-                number=1, title="T", html_url="u",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="t",
-            ),
-        ]
-        report = generate_report(items, [], [], label_suggestions=None)
-        assert "Suggested Labels" not in report
-
-    def test_label_concentration_warning(self):
-        """When >50% of suggestions point to the same label, a warning should appear."""
-        items = [
-            TriageItem(
-                number=i, title=f"Item {i}", html_url=f"https://example.com/{i}",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text=f"text {i}",
-            )
-            for i in range(4)
-        ]
-        # 3 out of 4 items get "bug" label -> 75% concentration
-        suggestions = [
-            [("bug", 0.85)],
-            [("bug", 0.80)],
-            [("bug", 0.75)],
-            [("enhancement", 0.90)],
-        ]
-        report = generate_report(items, [], [], label_suggestions=suggestions)
-        assert "Warning" in report
-        assert "`bug`" in report
-        assert "3/4" in report
-
-
-class TestMain:
-    """Tests for the main orchestration function."""
-
-    @patch.dict(os.environ, {"GITHUB_TOKEN": "", "GITHUB_REPOSITORY": "owner/repo"})
-    def test_missing_token_exits(self):
-        with pytest.raises(SystemExit) as exc_info:
-            main()
-        assert exc_info.value.code == 1
-
-    @patch.dict(os.environ, {"GITHUB_TOKEN": "tok", "GITHUB_REPOSITORY": ""})
-    def test_missing_repo_exits(self):
-        with pytest.raises(SystemExit) as exc_info:
-            main()
-        assert exc_info.value.code == 1
-
-    @patch("sweep.write_report")
-    @patch("sweep.fetch_all_open_items", return_value=[])
-    def test_no_items(self, mock_fetch, mock_write):
-        main()
-        mock_write.assert_called_once()
-        report = mock_write.call_args[0][0]
-        assert "No open issues or PRs found" in report
-
-    @patch("sweep.create_report_issue")
-    @patch("sweep.write_report")
-    @patch("sweep.suggest_labels", return_value=[])
-    @patch("sweep.find_duplicate_pairs", return_value=[])
-    @patch("sweep.detect_outliers", return_value=[])
-    @patch("sweep.reduce_dimensions")
-    @patch("sweep.normalize_rows")
-    @patch("sweep.embed_texts")
-    @patch("sweep.fetch_repo_labels")
-    @patch("sweep.fetch_all_open_items")
-    def test_full_flow_with_enough_items(
-        self, mock_fetch, mock_labels, mock_embed, mock_norm, mock_reduce,
-        mock_outliers, mock_dupes, mock_suggest, mock_write, mock_create,
-    ):
-        """Test the full flow with >= MIN_SAMPLES items (outlier detection runs)."""
-        n = MIN_SAMPLES_FOR_OUTLIER_DETECTION
-        items = [
-            TriageItem(
-                number=i, title=f"Item {i}", html_url=f"https://example.com/{i}",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text=f"text {i}",
-            )
-            for i in range(n)
-        ]
-        mock_fetch.return_value = items
-        mock_labels.return_value = [
-            RepoLabel(name="bug", description="Something broken", text="bug: Something broken"),
-        ]
-
-        embeddings = np.random.randn(n, 384).astype(np.float32)
-        mock_embed.return_value = embeddings
-        mock_norm.return_value = embeddings
-        mock_reduce.return_value = np.random.randn(n, 10).astype(np.float32)
-
-        main()
-
-        mock_fetch.assert_called_once()
-        mock_labels.assert_called_once()
-        # embed_texts called twice: once for items, once for labels
-        assert mock_embed.call_count == 2
-        mock_norm.assert_called()
-        mock_reduce.assert_called_once()
-        mock_outliers.assert_called_once()
-        mock_dupes.assert_called_once()
-        mock_suggest.assert_called_once()
-        mock_write.assert_called_once()
-        mock_create.assert_called_once()
-
-    @patch("sweep.create_report_issue")
-    @patch("sweep.write_report")
-    @patch("sweep.suggest_labels", return_value=[])
-    @patch("sweep.find_duplicate_pairs", return_value=[])
-    @patch("sweep.detect_outliers")
-    @patch("sweep.reduce_dimensions")
-    @patch("sweep.normalize_rows")
-    @patch("sweep.embed_texts")
-    @patch("sweep.fetch_repo_labels", return_value=[])
-    @patch("sweep.fetch_all_open_items")
-    def test_skips_outlier_detection_for_few_items(
-        self, mock_fetch, mock_labels, mock_embed, mock_norm, mock_reduce,
-        mock_outliers, mock_dupes, mock_suggest, mock_write, mock_create,
-    ):
-        """With < MIN_SAMPLES items, outlier detection should be skipped."""
-        n = MIN_SAMPLES_FOR_OUTLIER_DETECTION - 1
-        items = [
-            TriageItem(
-                number=i, title=f"Item {i}", html_url=f"https://example.com/{i}",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text=f"text {i}",
-            )
-            for i in range(n)
-        ]
-        mock_fetch.return_value = items
-
-        embeddings = np.random.randn(n, 384).astype(np.float32)
-        mock_embed.return_value = embeddings
-        mock_norm.return_value = embeddings
-
-        main()
-
-        # Outlier detection should not have been called
-        mock_reduce.assert_not_called()
-        mock_outliers.assert_not_called()
-        # But duplicates should still be checked
-        mock_dupes.assert_called_once()
-
-    @patch.dict(os.environ, {"INPUT_DRY_RUN": "true"})
-    @patch("sweep.DRY_RUN", True)
-    @patch("sweep.write_report")
-    @patch("sweep.create_report_issue")
-    @patch("sweep.apply_labels_to_item")
-    @patch("sweep.suggest_labels", return_value=[[("bug", 0.85)]])
-    @patch("sweep.find_duplicate_pairs", return_value=[])
-    @patch("sweep.normalize_rows")
-    @patch("sweep.embed_texts")
-    @patch("sweep.fetch_repo_labels")
-    @patch("sweep.fetch_all_open_items")
-    def test_dry_run_skips_issue_creation_and_labeling(
-        self, mock_fetch, mock_labels, mock_embed, mock_norm,
-        mock_dupes, mock_suggest, mock_apply, mock_create, mock_write,
-    ):
-        items = [
-            TriageItem(
-                number=1, title="Item", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="text",
-            )
-        ]
-        mock_fetch.return_value = items
-        mock_labels.return_value = [
-            RepoLabel(name="bug", description="Broken", text="bug: Broken"),
-        ]
-        embeddings = np.random.randn(1, 384).astype(np.float32)
-        mock_embed.return_value = embeddings
-        mock_norm.return_value = embeddings
-
-        main()
-
-        mock_create.assert_not_called()
-        mock_apply.assert_not_called()
-        mock_write.assert_called_once()
-
-    @patch("sweep.create_report_issue")
-    @patch("sweep.write_report")
-    @patch("sweep.apply_labels_to_item")
-    @patch("sweep.suggest_labels")
-    @patch("sweep.find_duplicate_pairs", return_value=[])
-    @patch("sweep.normalize_rows")
-    @patch("sweep.embed_texts")
-    @patch("sweep.fetch_repo_labels")
-    @patch("sweep.fetch_all_open_items")
-    def test_labels_not_auto_applied(
-        self, mock_fetch, mock_labels, mock_embed, mock_norm,
-        mock_dupes, mock_suggest, mock_apply, mock_write, mock_create,
-    ):
-        """Auto-labeling is disabled; labels should appear in report only."""
-        items = [
-            TriageItem(
-                number=1, title="Crash bug", html_url="https://example.com/1",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text="crash",
-            ),
-            TriageItem(
-                number=2, title="Already labeled", html_url="https://example.com/2",
-                is_pr=False, labels=["enhancement"], created_at="2026-01-01T00:00:00Z", text="feat",
-            ),
-        ]
-        mock_fetch.return_value = items
-        mock_labels.return_value = [
-            RepoLabel(name="bug", description="Broken", text="bug: Broken"),
-        ]
-        mock_suggest.return_value = [
-            [("bug", 0.90)],
-            [("bug", 0.45)],
-        ]
-
-        embeddings = np.random.randn(2, 384).astype(np.float32)
-        mock_embed.return_value = embeddings
-        mock_norm.return_value = embeddings
-
-        main()
-
-        # Auto-labeling is disabled — apply_labels_to_item should never be called
-        mock_apply.assert_not_called()
-
-    @patch("sweep.create_report_issue")
-    @patch("sweep.write_report")
-    @patch("sweep.apply_labels_to_item")
-    @patch("sweep.suggest_labels")
-    @patch("sweep.find_duplicate_pairs", return_value=[])
-    @patch("sweep.detect_outliers")
-    @patch("sweep.reduce_dimensions")
-    @patch("sweep.normalize_rows")
-    @patch("sweep.embed_texts")
-    @patch("sweep.fetch_repo_labels")
-    @patch("sweep.fetch_all_open_items")
-    def test_outliers_excluded_from_report_suggestions(
-        self, mock_fetch, mock_labels, mock_embed, mock_norm, mock_reduce,
-        mock_outliers, mock_dupes, mock_suggest, mock_apply, mock_write, mock_create,
-    ):
-        """Items flagged as outliers should not appear in report label suggestions."""
-        n = MIN_SAMPLES_FOR_OUTLIER_DETECTION
-        items = [
-            TriageItem(
-                number=i, title=f"Item {i}", html_url=f"https://example.com/{i}",
-                is_pr=False, labels=[], created_at="2026-01-01T00:00:00Z", text=f"text {i}",
-            )
-            for i in range(n)
-        ]
-        mock_fetch.return_value = items
-        mock_labels.return_value = [
-            RepoLabel(name="bug", description="Broken", text="bug: Broken"),
-        ]
-        mock_outliers.return_value = [(0, 12.5), (5, 15.3)]
-        mock_suggest.return_value = [[("bug", 0.85)] for _ in range(n)]
-
-        embeddings = np.random.randn(n, 384).astype(np.float32)
-        mock_embed.return_value = embeddings
-        mock_norm.return_value = embeddings
-        mock_reduce.return_value = np.random.randn(n, 10).astype(np.float32)
-
-        main()
-
-        # Auto-labeling is disabled
-        mock_apply.assert_not_called()
-        # Report should still be generated (outliers excluded from suggestions in report)
-        mock_write.assert_called_once()
-        report = mock_write.call_args[0][0]
-        # Outlier items 0 and 5 should not appear in the label suggestions section
-        assert "Item 0" not in report.split("Suggested Labels")[1] if "Suggested Labels" in report else True

.github/workflows/ci-quality.yml

@@ -1,14 +0,0 @@
-name: Quality Checks
-
-on:
-  workflow_call:
-
-jobs:
-  typecheck:
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: ./.github/actions/setup-gitnexus
-      - run: npx tsc --noEmit
-        working-directory: gitnexus

.github/workflows/ci-report.yml

@@ -1,348 +0,0 @@
-name: CI Report
-
-on:
-  workflow_run:
-    workflows: ['CI']
-    types: [completed]
-
-permissions:
-  actions: read
-  contents: read
-  pull-requests: write
-
-jobs:
-  pr-report:
-    name: PR Report
-    if: >-
-      github.event.workflow_run.event == 'pull_request' &&
-      github.event.workflow_run.conclusion != 'cancelled'
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-      - name: Download PR metadata
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        with:
-          script: |
-            const fs = require('fs');
-            const path = require('path');
-
-            const artifacts = await github.rest.actions.listWorkflowRunArtifacts({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }},
-            });
-
-            const meta = artifacts.data.artifacts.find(a => a.name === 'pr-meta');
-            if (!meta) {
-              core.setFailed('pr-meta artifact not found — skipping report');
-              return;
-            }
-
-            const zip = await github.rest.actions.downloadArtifact({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              artifact_id: meta.id,
-              archive_format: 'zip',
-            });
-
-            const dest = path.join(process.env.RUNNER_TEMP, 'pr-meta');
-            fs.mkdirSync(dest, { recursive: true });
-            fs.writeFileSync(path.join(dest, 'pr-meta.zip'), Buffer.from(zip.data));
-
-      - name: Extract PR metadata
-        id: meta
-        shell: bash
-        run: |
-          cd "$RUNNER_TEMP/pr-meta"
-          unzip -o pr-meta.zip
-
-          PR_NUMBER=$(cat pr-number | tr -d '[:space:]')
-          if ! [[ "$PR_NUMBER" =~ ^[0-9]+$ ]]; then
-            echo "::error::Invalid PR number: '$PR_NUMBER'"
-            exit 1
-          fi
-
-          echo "pr-number=$PR_NUMBER"         >> "$GITHUB_OUTPUT"
-          echo "quality=$(cat quality-result | tr -d '[:space:]')" >> "$GITHUB_OUTPUT"
-          echo "tests=$(cat tests-result | tr -d '[:space:]')"     >> "$GITHUB_OUTPUT"
-
-      - name: Download test reports
-        id: download-test-reports
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        with:
-          script: |
-            const fs = require('fs');
-            const path = require('path');
-
-            const artifacts = await github.rest.actions.listWorkflowRunArtifacts({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }},
-            });
-
-            const reports = artifacts.data.artifacts.find(a => a.name === 'test-reports');
-            if (!reports) {
-              core.warning('test-reports artifact not found');
-              return;
-            }
-
-            const zip = await github.rest.actions.downloadArtifact({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              artifact_id: reports.id,
-              archive_format: 'zip',
-            });
-
-            const dest = path.join(process.env.RUNNER_TEMP, 'test-reports');
-            fs.mkdirSync(dest, { recursive: true });
-            fs.writeFileSync(path.join(dest, 'test-reports.zip'), Buffer.from(zip.data));
-
-      - name: Extract test reports
-        if: steps.download-test-reports.outcome == 'success'
-        shell: bash
-        run: |
-          cd "$RUNNER_TEMP/test-reports"
-          unzip -o test-reports.zip || true
-
-      - name: Fetch cross-platform job results
-        id: jobs
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        with:
-          script: |
-            const jobs = await github.rest.actions.listJobsForWorkflowRun({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }},
-              per_page: 50,
-            });
-
-            const results = {};
-            for (const job of jobs.data.jobs) {
-              if (job.name.includes('ubuntu')) results.ubuntu = job.conclusion || 'pending';
-              else if (job.name.includes('windows')) results.windows = job.conclusion || 'pending';
-              else if (job.name.includes('macos')) results.macos = job.conclusion || 'pending';
-            }
-            core.setOutput('ubuntu', results.ubuntu || 'unknown');
-            core.setOutput('windows', results.windows || 'unknown');
-            core.setOutput('macos', results.macos || 'unknown');
-
-      - name: Fetch base branch coverage
-        id: base-coverage
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        with:
-          script: |
-            const fs = require('fs');
-            const path = require('path');
-
-            const runs = await github.rest.actions.listWorkflowRuns({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              workflow_id: 'ci.yml',
-              branch: 'main',
-              status: 'success',
-              per_page: 1,
-            });
-
-            if (runs.data.workflow_runs.length === 0) {
-              core.setOutput('found', 'false');
-              return;
-            }
-
-            const mainRunId = runs.data.workflow_runs[0].id;
-            const artifacts = await github.rest.actions.listWorkflowRunArtifacts({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: mainRunId,
-            });
-
-            const testReports = artifacts.data.artifacts.find(a => a.name === 'test-reports');
-            if (!testReports) {
-              core.setOutput('found', 'false');
-              return;
-            }
-
-            const zip = await github.rest.actions.downloadArtifact({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              artifact_id: testReports.id,
-              archive_format: 'zip',
-            });
-
-            const dest = path.join(process.env.RUNNER_TEMP, 'base-coverage');
-            fs.mkdirSync(dest, { recursive: true });
-            fs.writeFileSync(path.join(dest, 'base.zip'), Buffer.from(zip.data));
-            core.setOutput('found', 'true');
-            core.setOutput('dir', dest);
-
-      - name: Extract base coverage
-        if: steps.base-coverage.outputs.found == 'true'
-        shell: bash
-        run: |
-          cd "${{ steps.base-coverage.outputs.dir }}"
-          unzip -o base.zip -d base
-
-      - name: Build and post report
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        env:
-          PR_NUMBER: ${{ steps.meta.outputs.pr-number }}
-          QUALITY: ${{ steps.meta.outputs.quality }}
-          TESTS: ${{ steps.meta.outputs.tests }}
-          UBUNTU: ${{ steps.jobs.outputs.ubuntu }}
-          WINDOWS: ${{ steps.jobs.outputs.windows }}
-          MACOS: ${{ steps.jobs.outputs.macos }}
-          BASE_FOUND: ${{ steps.base-coverage.outputs.found }}
-          BASE_DIR: ${{ steps.base-coverage.outputs.dir }}
-          RUN_ID: ${{ github.event.workflow_run.id }}
-          HEAD_SHA: ${{ github.event.workflow_run.head_sha }}
-        with:
-          script: |
-            const fs = require('fs');
-            const path = require('path');
-
-            const icon = (s) => ({ success: '✅', failure: '❌', cancelled: '⏭️' }[s] || '❓');
-            const temp = process.env.RUNNER_TEMP;
-
-            // ── Read coverage ──
-            function readCov(dir) {
-              const out = { stmts: 'N/A', branch: 'N/A', funcs: 'N/A', lines: 'N/A',
-                            stmtsCov: '', branchCov: '', funcsCov: '', linesCov: '' };
-              try {
-                const files = require('child_process')
-                  .execSync(`find "${dir}" -name coverage-summary.json -type f`, { encoding: 'utf8' })
-                  .trim().split('\n').filter(Boolean);
-                if (!files.length) return out;
-                const d = JSON.parse(fs.readFileSync(files[0], 'utf8')).total;
-                out.stmts = d.statements.pct; out.branch = d.branches.pct;
-                out.funcs = d.functions.pct;  out.lines = d.lines.pct;
-                out.stmtsCov = `${d.statements.covered}/${d.statements.total}`;
-                out.branchCov = `${d.branches.covered}/${d.branches.total}`;
-                out.funcsCov = `${d.functions.covered}/${d.functions.total}`;
-                out.linesCov = `${d.lines.covered}/${d.lines.total}`;
-              } catch {}
-              return out;
-            }
-
-            const cov = readCov(path.join(temp, 'test-reports'));
-            const base = process.env.BASE_FOUND === 'true'
-              ? readCov(path.join(process.env.BASE_DIR, 'base'))
-              : { stmts: 'N/A', branch: 'N/A', funcs: 'N/A', lines: 'N/A' };
-
-            // ── Read test results ──
-            let total = 0, passed = 0, failed = 0, skipped = 0, suites = 0, duration = '0s';
-            let skippedTests = [];
-            try {
-              const files = require('child_process')
-                .execSync(`find "${path.join(temp, 'test-reports')}" -name test-results.json -type f`, { encoding: 'utf8' })
-                .trim().split('\n').filter(Boolean);
-              if (files.length) {
-                const r = JSON.parse(fs.readFileSync(files[0], 'utf8'));
-                total = r.numTotalTests || 0;
-                passed = r.numPassedTests || 0;
-                failed = r.numFailedTests || 0;
-                skipped = r.numPendingTests || 0;
-                suites = r.numTotalTestSuites || 0;
-                const durS = Math.floor((Math.max(...r.testResults.map(t => t.endTime)) - r.startTime) / 1000);
-                duration = durS >= 60 ? `${Math.floor(durS / 60)}m ${durS % 60}s` : `${durS}s`;
-                // Collect skipped test names
-                for (const suite of r.testResults) {
-                  for (const t of (suite.assertionResults || [])) {
-                    if (t.status === 'pending' || t.status === 'skipped') {
-                      skippedTests.push(`- ${t.ancestorTitles.join(' > ')} > ${t.title}`);
-                    }
-                  }
-                }
-              }
-            } catch {}
-
-            // ── Coverage delta ──
-            function delta(pct, basePct) {
-              if (pct === 'N/A' || basePct === 'N/A') return '—';
-              const d = (pct - basePct).toFixed(1);
-              const dNum = parseFloat(d);
-              if (dNum > 0) return `📈 +${d}%`;
-              if (dNum < 0) return `📉 ${d}%`;
-              return '＝';
-            }
-
-            // ── Build markdown ──
-            const { PR_NUMBER, QUALITY, TESTS, UBUNTU, WINDOWS, MACOS, RUN_ID, HEAD_SHA } = process.env;
-            const prNumber = parseInt(PR_NUMBER, 10);
-            const overall = (QUALITY === 'success' && TESTS === 'success')
-              ? '✅ **All checks passed**' : '❌ **Some checks failed**';
-            const sha = HEAD_SHA.slice(0, 7);
-
-            let body = `## CI Report\n\n${overall} &ensp; \`${sha}\`\n\n`;
-
-            body += `### Pipeline\n\n`;
-            body += `| Stage | Status | Ubuntu | Windows | macOS |\n`;
-            body += `|-------|--------|--------|---------|-------|\n`;
-            body += `| Typecheck | ${icon(QUALITY)} \`${QUALITY}\` | — | — | — |\n`;
-            body += `| Tests | ${icon(TESTS)} \`${TESTS}\` | ${icon(UBUNTU)} | ${icon(WINDOWS)} | ${icon(MACOS)} |\n\n`;
-
-            if (total > 0) {
-              body += `### Tests\n\n`;
-              body += `| Metric | Value |\n|--------|-------|\n`;
-              body += `| Total | **${total}** |\n`;
-              body += `| Passed | **${passed}** |\n`;
-              if (failed > 0) body += `| Failed | **${failed}** |\n`;
-              if (skipped > 0) body += `| Skipped | ${skipped} |\n`;
-              body += `| Files | ${suites} |\n`;
-              body += `| Duration | ${duration} |\n\n`;
-
-              if (failed === 0) {
-                body += `✅ All **${passed}** tests passed across **${suites}** files\n`;
-              } else {
-                body += `❌ **${failed}** failed / **${passed}** passed\n`;
-              }
-
-              if (skippedTests.length > 0) {
-                body += `\n<details>\n<summary>${skipped} test(s) skipped</summary>\n\n`;
-                body += skippedTests.join('\n') + '\n\n</details>\n';
-              }
-              body += '\n';
-            }
-
-            if (cov.stmts !== 'N/A') {
-              body += `### Coverage\n\n`;
-              body += `| Metric | Coverage | Covered | Base (main) | Delta |\n`;
-              body += `|--------|----------|---------|-------------|-------|\n`;
-              body += `| Statements | **${cov.stmts}%** | ${cov.stmtsCov} | ${base.stmts}% | ${delta(cov.stmts, base.stmts)} |\n`;
-              body += `| Branches | **${cov.branch}%** | ${cov.branchCov} | ${base.branch}% | ${delta(cov.branch, base.branch)} |\n`;
-              body += `| Functions | **${cov.funcs}%** | ${cov.funcsCov} | ${base.funcs}% | ${delta(cov.funcs, base.funcs)} |\n`;
-              body += `| Lines | **${cov.lines}%** | ${cov.linesCov} | ${base.lines}% | ${delta(cov.lines, base.lines)} |\n\n`;
-            } else {
-              const runUrl = `${context.serverUrl}/${context.repo.owner}/${context.repo.repo}/actions/runs/${RUN_ID}`;
-              body += `### Coverage\n\n⚠️ Coverage data unavailable — check the [test job](${runUrl}) for details.\n\n`;
-            }
-
-            const runUrl = `${context.serverUrl}/${context.repo.owner}/${context.repo.repo}/actions/runs/${RUN_ID}`;
-            body += `---\n<sub>📋 [Full run](${runUrl}) · Coverage from Ubuntu · Generated by CI</sub>`;
-
-            // ── Post sticky comment ──
-            const { data: comments } = await github.rest.issues.listComments({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              issue_number: prNumber,
-              per_page: 100,
-              direction: 'desc',
-            });
-
-            const marker = '<!-- ci-report -->';
-            const existing = comments.find(c => c.body?.includes(marker));
-            const fullBody = marker + '\n' + body;
-
-            if (existing) {
-              await github.rest.issues.updateComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                comment_id: existing.id,
-                body: fullBody,
-              });
-            } else {
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: prNumber,
-                body: fullBody,
-              });
-            }

.github/workflows/ci-tests.yml

@@ -1,57 +0,0 @@
-name: Tests
-
-on:
-  workflow_call:
-
-jobs:
-  tests:
-    name: ubuntu / coverage
-    runs-on: ubuntu-latest
-    timeout-minutes: 25
-    steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: ./.github/actions/setup-gitnexus
-        with:
-          build: 'true'
-
-      - name: Run all tests with coverage
-        run: >-
-          npx vitest run
-          --reporter=default
-          --reporter=json
-          --outputFile=test-results.json
-          --coverage
-          --coverage.reporter=json-summary
-          --coverage.reporter=json
-          --coverage.reporter=text
-          --coverage.thresholdAutoUpdate=false
-          --coverage.reportOnFailure=true
-        working-directory: gitnexus
-
-      - name: Upload test reports
-        if: always()
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
-        with:
-          name: test-reports
-          path: |
-            gitnexus/coverage/coverage-summary.json
-            gitnexus/coverage/coverage-final.json
-            gitnexus/test-results.json
-          retention-days: 5
-
-  cross-platform:
-    name: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        # Ubuntu already covered by the coverage job above
-        os: [windows-latest, macos-latest]
-    runs-on: ${{ matrix.os }}
-    timeout-minutes: 25
-    steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: ./.github/actions/setup-gitnexus
-        with:
-          build: 'true'
-      - run: npx vitest run
-        working-directory: gitnexus

.github/workflows/ci.yml

@@ -3,81 +3,67 @@ name: CI
 on:
   push:
     branches: [main]
-    paths-ignore: ['**.md', 'docs/**', 'LICENSE']
   pull_request:
     branches: [main]
-    paths-ignore: ['**.md', 'docs/**', 'LICENSE']
   workflow_call:
 
-concurrency:
-  group: ci-${{ github.ref }}
-  cancel-in-progress: true
-
-# ── Reusable workflow orchestration ─────────────────────────────────
-# Each concern lives in its own workflow file for maintainability:
-#   ci-quality.yml       — typecheck (tsc --noEmit)
-#   ci-tests.yml         — all tests with coverage (ubuntu) + cross-platform
-#   ci-report.yml        — PR comment (workflow_run trigger for fork write access)
-
 jobs:
-  quality:
-    uses: ./.github/workflows/ci-quality.yml
-    permissions:
-      contents: read
-
-  tests:
-    uses: ./.github/workflows/ci-tests.yml
-    permissions:
-      contents: read
-
-  # ── Unified CI gate ──────────────────────────────────────────────
-  # Single required check for branch protection.
-  ci-status:
-    name: CI Gate
-    needs: [quality, tests]
-    if: always()
+  typecheck:
     runs-on: ubuntu-latest
-    timeout-minutes: 5
     steps:
-      - name: Check all jobs passed
-        shell: bash
-        env:
-          QUALITY: ${{ needs.quality.result }}
-          TESTS: ${{ needs.tests.result }}
-        run: |
-          echo "Quality:  $QUALITY"
-          echo "Tests:    $TESTS"
-          if [[ "$QUALITY" != "success" ]] ||
-             [[ "$TESTS" != "success" ]]; then
-            echo "::error::One or more CI jobs failed"
-            exit 1
-          fi
-
-  # ── PR metadata for ci-report.yml ────────────────────────────────
-  # Saves PR number and job results so the workflow_run-triggered
-  # report can post comments with a write token (works for forks).
-  save-pr-meta:
-    name: Save PR Metadata
-    if: always() && github.event_name == 'pull_request'
-    needs: [quality, tests]
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-      - name: Write PR metadata
-        shell: bash
-        env:
-          PR_NUMBER: ${{ github.event.pull_request.number }}
-          QUALITY: ${{ needs.quality.result }}
-          TESTS: ${{ needs.tests.result }}
-        run: |
-          mkdir -p pr-meta
-          echo "$PR_NUMBER" > pr-meta/pr-number
-          echo "$QUALITY"   > pr-meta/quality-result
-          echo "$TESTS"     > pr-meta/tests-result
-
-      - name: Upload PR metadata
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          name: pr-meta
-          path: pr-meta/
-          retention-days: 1
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx tsc --noEmit
+        working-directory: gitnexus
+
+  unit-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/unit --coverage --coverage.thresholdAutoUpdate=false
+        working-directory: gitnexus
+
+  integration-tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/integration
+        working-directory: gitnexus
+
+  cross-platform:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm
+          cache-dependency-path: gitnexus/package-lock.json
+      - run: npm ci
+        working-directory: gitnexus
+      - run: npx vitest run test/unit
+        working-directory: gitnexus

.github/workflows/claude-code-review.yml

@@ -1,95 +1,44 @@
 name: Claude Code Review
 
-# Uses pull_request_target so the workflow runs as defined on the default branch,
-# which allows access to secrets for posting review comments on fork PRs.
-# SECURITY: The checkout pins the fork's HEAD SHA (not the branch name) to
-# prevent TOCTOU races (force-push between trigger and checkout). The
-# claude-code-action sandboxes execution — it does NOT run arbitrary code
-# from the checked-out source.
-
 on:
-  # Trigger only when explicitly requested:
-  #   - Add the "claude-review" label to a PR, OR
-  #   - Comment "@claude" or "/review" on a PR
-  pull_request_target:
-    types: [labeled]
-  issue_comment:
-    types: [created]
-
-# Serialize per-PR to avoid racing review comments.
-concurrency:
-  group: claude-review-${{ github.event.issue.number || github.event.pull_request.number }}
-  cancel-in-progress: false
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
 
 jobs:
   claude-review:
-    # Run only when:
-    #   1. The "claude-review" label is added to a non-draft PR by a trusted contributor, OR
-    #   2. A trusted contributor comments "@claude" or "/review" on a PR
-    if: |
-      (
-        github.event_name == 'pull_request_target' &&
-        github.event.label.name == 'claude-review' &&
-        github.event.pull_request.draft == false &&
-        (github.event.pull_request.author_association == 'OWNER' ||
-         github.event.pull_request.author_association == 'MEMBER' ||
-         github.event.pull_request.author_association == 'COLLABORATOR')
-      ) ||
-      (
-        github.event_name == 'issue_comment' &&
-        github.event.issue.pull_request &&
-        (contains(github.event.comment.body, '@claude') ||
-         contains(github.event.comment.body, '/review')) &&
-        (github.event.comment.author_association == 'OWNER' ||
-         github.event.comment.author_association == 'MEMBER' ||
-         github.event.comment.author_association == 'COLLABORATOR')
-      )
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
     runs-on: ubuntu-latest
-    timeout-minutes: 30
     permissions:
       contents: read
-      pull-requests: write
+      pull-requests: read
       issues: read
       id-token: write
 
     steps:
-      # For issue_comment triggers, resolve the PR number, head SHA, and fork repo
-      - name: Resolve PR context
-        id: pr
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+      - name: Checkout repository
+        uses: actions/checkout@v4
         with:
-          script: |
-            let pr;
-            if (context.eventName === 'issue_comment') {
-              const resp = await github.rest.pulls.get({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                pull_number: context.payload.issue.number,
-              });
-              pr = resp.data;
-            } else {
-              pr = context.payload.pull_request;
-            }
-            core.setOutput('number', pr.number);
-            core.setOutput('sha', pr.head.sha);
-            core.setOutput('repo', pr.head.repo.full_name);
-            core.setOutput('branch', pr.head.ref);
-
-      - name: Checkout PR head
-        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-        with:
-          repository: ${{ steps.pr.outputs.repo }}
-          ref: ${{ steps.pr.outputs.sha }}
           fetch-depth: 1
 
       - name: Run Claude Code Review
         id: claude-review
-        uses: anthropics/claude-code-action@9469d113c6afd29550c402740f22d1a97dd1209b # v1
+        uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          allowed_non_write_users: '*'
-          show_full_output: true
           plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
           plugins: 'code-review@claude-code-plugins'
-          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ steps.pr.outputs.number }}'
+          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+

.github/workflows/claude.yml

@@ -10,101 +10,41 @@ on:
   pull_request_review:
     types: [submitted]
 
-# Serialize per-PR/issue to avoid racing comments.
-concurrency:
-  group: claude-code-${{ github.event.issue.number || github.event.pull_request.number || github.event.issue.id }}
-  cancel-in-progress: false
-
 jobs:
   claude:
     if: |
-      (
-        github.event_name == 'issue_comment' &&
-        contains(github.event.comment.body, '@claude') &&
-        (github.event.comment.author_association == 'OWNER' ||
-         github.event.comment.author_association == 'MEMBER' ||
-         github.event.comment.author_association == 'COLLABORATOR')
-      ) ||
-      (
-        github.event_name == 'pull_request_review_comment' &&
-        contains(github.event.comment.body, '@claude') &&
-        (github.event.comment.author_association == 'OWNER' ||
-         github.event.comment.author_association == 'MEMBER' ||
-         github.event.comment.author_association == 'COLLABORATOR')
-      ) ||
-      (
-        github.event_name == 'pull_request_review' &&
-        contains(github.event.review.body, '@claude') &&
-        (github.event.review.author_association == 'OWNER' ||
-         github.event.review.author_association == 'MEMBER' ||
-         github.event.review.author_association == 'COLLABORATOR')
-      ) ||
-      (
-        github.event_name == 'issues' &&
-        (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')) &&
-        (github.event.issue.author_association == 'OWNER' ||
-         github.event.issue.author_association == 'MEMBER' ||
-         github.event.issue.author_association == 'COLLABORATOR')
-      )
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
     runs-on: ubuntu-latest
-    timeout-minutes: 30
     permissions:
       contents: read
-      pull-requests: write
-      issues: write
+      pull-requests: read
+      issues: read
       id-token: write
-      actions: read         # required for Claude to read CI results on PRs
+      actions: read # Required for Claude to read CI results on PRs
     steps:
-      # For PR-related triggers, resolve the fork repo so we can checkout correctly.
-      - name: Resolve PR context
-        id: pr
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        with:
-          script: |
-            // Determine if this event is PR-related
-            let prNumber = null;
-            if (context.eventName === 'issue_comment' && context.payload.issue.pull_request) {
-              prNumber = context.payload.issue.number;
-            } else if (context.eventName === 'pull_request_review_comment') {
-              prNumber = context.payload.pull_request.number;
-            } else if (context.eventName === 'pull_request_review') {
-              prNumber = context.payload.pull_request.number;
-            }
-
-            if (!prNumber) {
-              core.setOutput('is_pr', 'false');
-              return;
-            }
-
-            const resp = await github.rest.pulls.get({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              pull_number: prNumber,
-            });
-            const pr = resp.data;
-
-            core.setOutput('is_pr', 'true');
-            core.setOutput('number', String(prNumber));
-            core.setOutput('sha', pr.head.sha);
-            core.setOutput('repo', pr.head.repo.full_name);
-            core.setOutput('branch', pr.head.ref);
-
       - name: Checkout repository
-        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
+        uses: actions/checkout@v4
         with:
-          repository: ${{ steps.pr.outputs.is_pr == 'true' && steps.pr.outputs.repo || github.repository }}
-          ref: ${{ steps.pr.outputs.is_pr == 'true' && steps.pr.outputs.sha || '' }}
           fetch-depth: 1
 
       - name: Run Claude Code
         id: claude
-        uses: anthropics/claude-code-action@9469d113c6afd29550c402740f22d1a97dd1209b # v1
+        uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          allowed_non_write_users: '*'
-          show_full_output: true
 
           # This is an optional setting that allows Claude to read CI results on PRs
           additional_permissions: |
             actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          # claude_args: '--allowed-tools Bash(gh pr:*)'
+

.github/workflows/pr-description-check.yml

@@ -1,94 +0,0 @@
-name: PR Description Check
-
-on:
-  pull_request:
-    types: [opened, edited, reopened]
-    branches: [main]
-
-permissions:
-  pull-requests: write
-
-concurrency:
-  group: pr-desc-${{ github.event.pull_request.number }}
-  cancel-in-progress: true
-
-jobs:
-  check-description:
-    runs-on: ubuntu-latest
-    timeout-minutes: 5
-    steps:
-      - name: Check PR description quality
-        uses: actions/github-script@ed597411d8f924073f98dfc5c65a23a2325f34cd # v8
-        with:
-          script: |
-            const MIN_BODY_LENGTH = 50;
-            const LABEL = 'needs-description';
-
-            const pr = context.payload.pull_request;
-            const body = (pr.body || '').trim();
-            const owner = context.repo.owner;
-            const repo = context.repo.repo;
-            const number = pr.number;
-
-            const hasLabel = pr.labels.some(l => l.name === LABEL);
-
-            if (body.length < MIN_BODY_LENGTH) {
-              // Add label if not already present
-              if (!hasLabel) {
-                await github.rest.issues.addLabels({
-                  owner, repo, issue_number: number,
-                  labels: [LABEL],
-                });
-              }
-
-              // Post or update a comment
-              const marker = '<!-- pr-desc-check -->';
-              const message = [
-                marker,
-                `### PR description is too short`,
-                '',
-                `This PR's description is **${body.length}** characters, ` +
-                `but the minimum is **${MIN_BODY_LENGTH}**.`,
-                '',
-                'Please update the PR description to explain:',
-                '- **What** this PR changes',
-                '- **Why** the change is needed',
-                '',
-                'Use the PR template as a guide. This check will re-run when you edit the description.',
-              ].join('\n');
-
-              // Find existing bot comment to update (avoid spam)
-              const comments = await github.rest.issues.listComments({
-                owner, repo, issue_number: number,
-              });
-              const existing = comments.data.find(c =>
-                c.body && c.body.includes(marker)
-              );
-
-              if (existing) {
-                await github.rest.issues.updateComment({
-                  owner, repo, comment_id: existing.id,
-                  body: message,
-                });
-              } else {
-                await github.rest.issues.createComment({
-                  owner, repo, issue_number: number,
-                  body: message,
-                });
-              }
-
-              core.setFailed(
-                `PR description is ${body.length} chars (minimum: ${MIN_BODY_LENGTH})`
-              );
-            } else {
-              // Description is acceptable — remove the label if present
-              if (hasLabel) {
-                await github.rest.issues.removeLabel({
-                  owner, repo, issue_number: number,
-                  name: LABEL,
-                }).catch(() => {});
-                // .catch: label may have been removed manually
-              }
-
-              core.info(`PR description OK (${body.length} chars)`);
-            }

.github/workflows/publish.yml

@@ -5,26 +5,19 @@ on:
     tags:
       - 'v*'
 
-# No workflow-level permissions — scoped per job below.
-
 jobs:
   ci:
     uses: ./.github/workflows/ci.yml
-    permissions:
-      contents: read
-      actions: read
-      pull-requests: write
 
   publish:
     needs: ci
     runs-on: ubuntu-latest
-    timeout-minutes: 15
     permissions:
       contents: write
       id-token: write
     steps:
-      - uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-      - uses: actions/setup-node@49933ea5288caeca8642d1e84afbd3f7d6820020 # v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: 20
           registry-url: https://registry.npmjs.org
@@ -34,13 +27,8 @@ jobs:
         working-directory: gitnexus
 
       - name: Verify version consistency
-        shell: bash
         run: |
           TAG_VERSION="${GITHUB_REF#refs/tags/v}"
-          if ! [[ "$TAG_VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$ ]]; then
-            echo "::error::Tag does not follow semver: v$TAG_VERSION"
-            exit 1
-          fi
           PKG_VERSION=$(node -p "require('./package.json').version")
           if [ "$TAG_VERSION" != "$PKG_VERSION" ]; then
             echo "::error::Tag version (v$TAG_VERSION) does not match package.json version ($PKG_VERSION)"
@@ -64,6 +52,6 @@ jobs:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
 
       - name: Create GitHub Release
-        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2
+        uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true

.github/workflows/triage-sweep.yml

@@ -1,103 +0,0 @@
-name: Triage Sweep
-
-on:
-  workflow_dispatch:
-    inputs:
-      iqr_multiplier:
-        description: >-
-          IQR multiplier for outlier cutoff.
-          cutoff = Q75 + multiplier * IQR.
-          Higher = fewer outliers flagged.
-        type: number
-        default: 3.0
-      max_outlier_pct:
-        description: >-
-          Maximum fraction of items that can be flagged as outliers (0-1).
-          Hard cap to prevent over-flagging.
-        type: number
-        default: 0.05
-      contamination:
-        description: >-
-          Expected fraction of outliers in the data (0-0.5).
-          Controls how aggressively EllipticEnvelope downweights extremes.
-        type: number
-        default: 0.1
-      cosine_threshold:
-        description: >-
-          Cosine similarity threshold for duplicate detection.
-          Pairs with similarity above this are flagged as potential duplicates.
-          Higher = only very similar pairs flagged.
-        type: number
-        default: 0.92
-      max_items:
-        description: >-
-          Maximum number of open issues + PRs to process.
-          Hard cap to prevent runaway costs on very large repos.
-        type: number
-        default: 500
-      dry_run:
-        description: >-
-          Check this to only log results to the workflow summary.
-          Uncheck to create a GitHub issue with the report and apply labels.
-        type: boolean
-        default: false
-
-permissions:
-  contents: read
-  issues: write
-  pull-requests: write
-
-concurrency:
-  group: triage-sweep
-  cancel-in-progress: true
-
-jobs:
-  sweep:
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-        with:
-          sparse-checkout: .github/scripts/triage
-          sparse-checkout-cone-mode: false
-          fetch-depth: 1
-
-      - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
-        with:
-          python-version: '3.12'
-          cache: pip
-          cache-dependency-path: .github/scripts/triage/requirements.txt
-
-      - name: Install dependencies
-        run: pip install -r .github/scripts/triage/requirements.txt
-
-      - name: Cache FastEmbed model weights
-        uses: actions/cache@668228422ae6a00e4ad889ee87cd7109ec5666a7 # v5
-        with:
-          path: ${{ github.workspace }}/.fastembed_cache
-          key: fastembed-bge-small-en-v1.5
-
-      - name: Run triage sweep
-        id: sweep
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          GITHUB_REPOSITORY: ${{ github.repository }}
-          FASTEMBED_CACHE_PATH: ${{ github.workspace }}/.fastembed_cache
-          INPUT_IQR_MULTIPLIER: ${{ inputs.iqr_multiplier }}
-          INPUT_MAX_OUTLIER_PCT: ${{ inputs.max_outlier_pct }}
-          INPUT_CONTAMINATION: ${{ inputs.contamination }}
-          INPUT_COSINE_THRESHOLD: ${{ inputs.cosine_threshold }}
-          INPUT_MAX_ITEMS: ${{ inputs.max_items }}
-          INPUT_DRY_RUN: ${{ inputs.dry_run }}
-        run: python .github/scripts/triage/sweep.py
-
-      - name: Post summary
-        if: always()
-        run: |
-          if [ -f /tmp/triage-report.md ]; then
-            cat /tmp/triage-report.md >> "$GITHUB_STEP_SUMMARY"
-          else
-            echo "No report generated." >> "$GITHUB_STEP_SUMMARY"
-          fi

.gitignore

@@ -48,9 +48,6 @@ coverage/
 # Claude Code worktrees
 .claude/worktrees/
 
-# Claude code skills
-.claude/skills/generated/
-
 # Assets (screenshots, images)
 assets/
 
@@ -59,16 +56,3 @@ repomix-output*
 
 # Design docs (local only)
 docs/plans/
-
-gitnexus/test/fixtures/mini-repo/*.md
-gitnexus/test/fixtures/mini-repo/.claude
-gitnexus/test/fixtures/mini-repo/.gitignore
-
-# Ignore csharp generated obj and bin folders
-gitnexus/test/fixtures/lang-resolution/**/obj
-gitnexus/test/fixtures/lang-resolution/**/bin
-GitNexus.sln
-# Git worktrees
-.worktrees/
-
-/github/scripts/triage/__pycache__/

.history/gitnexus/vitest.config_20260317171253.ts

@@ -1,33 +0,0 @@
-import { defineConfig } from 'vitest/config';
-
-export default defineConfig({
-  test: {
-    globalSetup: ['test/global-setup.ts'],
-    include: ['test/**/*.test.ts'],
-    testTimeout: 30000,
-    hookTimeout: 120000,
-    pool: 'forks',
-    globals: true,
-    setupFiles: ['test/setup.ts'],
-    teardownTimeout: 3000,
-    dangerouslyIgnoreUnhandledErrors: true, // LadybugDB N-API destructor segfaults on fork exit — not a test failure
-    coverage: {
-      provider: 'v8',
-      include: ['src/**/*.ts'],
-      exclude: [
-        'src/cli/index.ts',          // CLI entry point (commander wiring)
-        'src/server/**',              // HTTP server (requires network)
-        'src/core/wiki/**',           // Wiki generation (requires LLM)
-      ],
-      // Auto-ratchet: vitest bumps thresholds when coverage exceeds them.
-      // CI will fail if a PR drops below these floors.
-      thresholds: {
-        statements: 26,
-        branches: 23,
-        functions: 28,
-        lines: 27,
-        autoUpdate: true,
-      },
-    },
-  },
-});

.husky/pre-commit

@@ -1,33 +0,0 @@
-#!/usr/bin/env bash
-# Pre-commit hook (husky): typecheck + unit tests for both packages.
-# Mirrors CI checks from ci-quality.yml and ci-tests.yml.
-# Skip with: git commit --no-verify
-#
-# CI coverage:
-#   quality / typecheck      → tsc --noEmit in gitnexus/
-#   quality / typecheck-web  → tsc -b --noEmit in gitnexus-web/
-#   tests / ubuntu+coverage  → vitest run in gitnexus/ (all projects)
-#   e2e / chromium           → playwright (requires servers — skipped)
-
-ROOT="$(git rev-parse --show-toplevel)"
-
-WEB_CHANGED=$(git diff --cached --name-only -- 'gitnexus-web/' | head -1)
-CLI_CHANGED=$(git diff --cached --name-only -- 'gitnexus/' | head -1)
-
-if [ -n "$WEB_CHANGED" ]; then
-  echo "pre-commit: typechecking gitnexus-web (tsc -b)..."
-  cd "$ROOT/gitnexus-web" && npx tsc -b --noEmit
-
-  echo "pre-commit: running gitnexus-web unit tests..."
-  npx vitest run --reporter=dot
-fi
-
-if [ -n "$CLI_CHANGED" ]; then
-  echo "pre-commit: typechecking gitnexus..."
-  cd "$ROOT/gitnexus" && npx tsc --noEmit
-
-  echo "pre-commit: running gitnexus unit tests (default project)..."
-  npx vitest run --project default --reporter=dot
-fi
-
-echo "pre-commit: all checks passed"

AGENTS.md

@@ -1,93 +1,17 @@
 <!-- gitnexus:start -->
-# GitNexus — Code Intelligence
+# GitNexus MCP
 
-This project is indexed by GitNexus as **GitNexus** (2273 symbols, 5419 relationships, 174 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+This project is indexed by GitNexus as **GitnexusV2** (1444 symbols, 3700 relationships, 111 execution flows).
 
-> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+## Always Start Here
 
-## Always Do
+1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
+2. **Match your task to a skill below** and **read that skill file**
+3. **Follow the skill's workflow and checklist**
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
-- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+> If step 1 warns the index is stale, run `npx gitnexus analyze` in the terminal first.
 
-## When Debugging
-
-1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
-2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
-3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
-4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed
-
-## When Refactoring
-
-- **Renaming**: MUST use `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with `dry_run: false`.
-- **Extracting/Splitting**: MUST run `gitnexus_context({name: "target"})` to see all incoming/outgoing refs, then `gitnexus_impact({target: "target", direction: "upstream"})` to find all external callers before moving code.
-- After any refactor: run `gitnexus_detect_changes({scope: "all"})` to verify only expected files changed.
-
-## Never Do
-
-- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
-- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
-- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
-
-## Tools Quick Reference
-
-| Tool | When to use | Command |
-|------|-------------|---------|
-| `query` | Find code by concept | `gitnexus_query({query: "auth validation"})` |
-| `context` | 360-degree view of one symbol | `gitnexus_context({name: "validateUser"})` |
-| `impact` | Blast radius before editing | `gitnexus_impact({target: "X", direction: "upstream"})` |
-| `detect_changes` | Pre-commit scope check | `gitnexus_detect_changes({scope: "staged"})` |
-| `rename` | Safe multi-file rename | `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` |
-| `cypher` | Custom graph queries | `gitnexus_cypher({query: "MATCH ..."})` |
-
-## Impact Risk Levels
-
-| Depth | Meaning | Action |
-|-------|---------|--------|
-| d=1 | WILL BREAK — direct callers/importers | MUST update these |
-| d=2 | LIKELY AFFECTED — indirect deps | Should test |
-| d=3 | MAY NEED TESTING — transitive | Test if critical path |
-
-## Resources
-
-| Resource | Use for |
-|----------|---------|
-| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
-| `gitnexus://repo/GitNexus/clusters` | All functional areas |
-| `gitnexus://repo/GitNexus/processes` | All execution flows |
-| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
-
-## Self-Check Before Finishing
-
-Before completing any code modification task, verify:
-1. `gitnexus_impact` was run for all modified symbols
-2. No HIGH/CRITICAL risk warnings were ignored
-3. `gitnexus_detect_changes()` confirms changes match expected scope
-4. All d=1 (WILL BREAK) dependents were updated
-
-## Keeping the Index Fresh
-
-After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
-
-```bash
-npx gitnexus analyze
-```
-
-If the index previously included embeddings, preserve them by adding `--embeddings`:
-
-```bash
-npx gitnexus analyze --embeddings
-```
-
-To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.embeddings` field shows the count (0 means no embeddings). **Running analyze without `--embeddings` will delete any previously generated embeddings.**
-
-> Claude Code users: A PostToolUse hook handles this automatically after `git commit` and `git merge`.
-
-## CLI
+## Skills
 
 | Task | Read this skill file |
 |------|---------------------|

CHANGELOG.md

@@ -1,109 +0,0 @@
-# Changelog
-
-All notable changes to GitNexus will be documented in this file.
-
-## [Unreleased]
-
-### Changed
-- Migrated from KuzuDB to LadybugDB v0.15 (`@ladybugdb/core`, `@ladybugdb/wasm-core`)
-- Renamed all internal paths from `kuzu` to `lbug` (storage: `.gitnexus/kuzu` → `.gitnexus/lbug`)
-- Added automatic cleanup of stale KuzuDB index files
-- LadybugDB v0.15 requires explicit VECTOR extension loading for semantic search
-
-## [1.4.0] - 2026-03-13
-
-### Added
-
-- **Language-aware symbol resolution engine** with 3-tier resolver: exact FQN → scope-walk → guarded fuzzy fallback that refuses ambiguous matches (#238) — @magyargergo
-- **Method Resolution Order (MRO)** with 5 language-specific strategies: C++ leftmost-base, C#/Java class-over-interface, Python C3 linearization, Rust qualified syntax, default BFS (#238) — @magyargergo
-- **Constructor & struct literal resolution** across all languages — `new Foo()`, `User{...}`, C# primary constructors, target-typed new (#238) — @magyargergo
-- **Receiver-constrained resolution** using per-file TypeEnv — disambiguates `user.save()` vs `repo.save()` via `ownerId` matching (#238) — @magyargergo
-- **Heritage & ownership edges** — HAS_METHOD, OVERRIDES, Go struct embedding, Swift extension heritage, method signatures (`parameterCount`, `returnType`) (#238) — @magyargergo
-- **Language-specific resolver directory** (`resolvers/`) — extracted JVM, Go, C#, PHP, Rust resolvers from monolithic import-processor (#238) — @magyargergo
-- **Type extractor directory** (`type-extractors/`) — per-language type binding extraction with `Record<SupportedLanguages, Handler>` + `satisfies` dispatch (#238) — @magyargergo
-- **Export detection dispatch table** — compile-time exhaustive `Record` + `satisfies` pattern replacing switch/if chains (#238) — @magyargergo
-- **Language config module** (`language-config.ts`) — centralized tsconfig, go.mod, composer.json, .csproj, Swift package config loaders (#238) — @magyargergo
-- **Optional skill generation** via `npx gitnexus analyze --skills` — generates AI agent skills from KuzuDB knowledge graph (#171) — @zander-raycraft
-- **First-class C# support** — sibling-based modifier scanning, record/delegate/property/field/event declaration types (#163, #170, #178 via #237) — @Alice523, @benny-yamagata, @jnMetaCode
-- **C/C++ support fixes** — `.h` → C++ mapping, static-linkage export detection, qualified/parenthesized declarators, 48 entry point patterns (#163, #227 via #237) — @Alice523, @bitgineer
-- **Rust support fixes** — sibling-based `visibility_modifier` scanning for `pub` detection (#227 via #237) — @bitgineer
-- **Adaptive tree-sitter buffer sizing** — `Math.min(Math.max(contentLength * 2, 512KB), 32MB)` (#216 via #237) — @JasonOA888
-- **Call expression matching** in tree-sitter queries (#234 via #237) — @ex-nihilo-jg
-- **DeepSeek model configurations** (#217) — @JasonOA888
-- 282+ new unit tests, 178 integration resolver tests across 9 languages, 53 test files, 1146 total tests passing
-
-### Fixed
-
-- Skip unavailable native Swift parsers in sequential ingestion (#188) — @Gujiassh
-- Heritage heuristic language-gated — no longer applies class/interface rules to wrong languages (#238) — @magyargergo
-- C# `base_list` distinguishes EXTENDS vs IMPLEMENTS via symbol table + `I[A-Z]` heuristic (#238) — @magyargergo
-- Go `qualified_type` (`models.User`) correctly unwrapped in TypeEnv (#238) — @magyargergo
-- Global tier no longer blocks resolution when kind/arity filtering can narrow to 1 candidate (#238) — @magyargergo
-
-### Changed
-
-- `import-processor.ts` reduced from 1412 → 711 lines (50% reduction) via resolver and config extraction (#238) — @magyargergo
-- `type-env.ts` reduced from 635 → ~125 lines via type-extractor extraction (#238) — @magyargergo
-- CI/CD workflows hardened with security fixes and fork PR support (#222, #225) — @magyargergo
-
-## [1.3.11] - 2026-03-08
-
-### Security
-
-- Fix FTS Cypher injection by escaping backslashes in search queries (#209) — @magyargergo
-
-### Added
-
-- Auto-reindex hook that runs `gitnexus analyze` after commits and merges, with automatic embeddings preservation (#205) — @L1nusB
-- 968 integration tests (up from ~840) covering unhappy paths across search, enrichment, CLI, pipeline, worker pool, and KuzuDB (#209) — @magyargergo
-- Coverage auto-ratcheting so thresholds bump automatically on CI (#209) — @magyargergo
-- Rich CI PR report with coverage bars, test counts, and threshold tracking (#209) — @magyargergo
-- Modular CI workflow architecture with separate unit-test, integration-test, and orchestrator jobs (#209) — @magyargergo
-
-### Fixed
-
-- KuzuDB native addon crashes on Linux/macOS by running integration tests in isolated vitest processes with `--pool=forks` (#209) — @magyargergo
-- Worker pool `MODULE_NOT_FOUND` crash when script path is invalid (#209) — @magyargergo
-
-### Changed
-
-- Added macOS to the cross-platform CI test matrix (#208) — @magyargergo
-
-## [1.3.10] - 2026-03-07
-
-### Security
-
-- **MCP transport buffer cap**: Added 10 MB `MAX_BUFFER_SIZE` limit to prevent out-of-memory attacks via oversized `Content-Length` headers or unbounded newline-delimited input
-- **Content-Length validation**: Reject `Content-Length` values exceeding the buffer cap before allocating memory
-- **Stack overflow prevention**: Replaced recursive `readNewlineMessage` with iterative loop to prevent stack overflow from consecutive empty lines
-- **Ambiguous prefix hardening**: Tightened `looksLikeContentLength` to require 14+ bytes before matching, preventing false framing detection on short input
-- **Closed transport guard**: `send()` now rejects with a clear error when called after `close()`, with proper write-error propagation
-
-### Added
-
-- **Dual-framing MCP transport** (`CompatibleStdioServerTransport`): Auto-detects Content-Length (Codex/OpenCode) and newline-delimited JSON (Cursor/Claude Code) framing on the first message, responds in the same format (#207)
-- **Lazy CLI module loading**: All CLI subcommands now use `createLazyAction()` to defer heavy imports (tree-sitter, ONNX, KuzuDB) until invocation, significantly improving `gitnexus mcp` startup time (#207)
-- **Type-safe lazy actions**: `createLazyAction` uses constrained generics to validate export names against module types at compile time
-- **Regression test suite**: 13 unit tests covering transport framing, security hardening, buffer limits, and lazy action loading
-
-### Fixed
-
-- **CALLS edge sourceId alignment**: `findEnclosingFunctionId` now generates IDs with `:startLine` suffix matching node creation format, fixing process detector finding 0 entry points (#194)
-- **LRU cache zero maxSize crash**: Guard `createASTCache` against `maxSize=0` when repos have no parseable files (#144)
-
-### Changed
-
-- Transport constructor accepts `NodeJS.ReadableStream` / `NodeJS.WritableStream` (widened from concrete `ReadStream`/`WriteStream`)
-- `processReadBuffer` simplified to break on first error instead of stale-buffer retry loop
-
-## [1.3.9] - 2026-03-06
-
-### Fixed
-
-- Aligned CALLS edge sourceId with node ID format in parse worker (#194)
-
-## [1.3.8] - 2026-03-05
-
-### Fixed
-
-- Force-exit after analyze to prevent KuzuDB native cleanup hang (#192)

CLAUDE.md

@@ -1,93 +1,17 @@
 <!-- gitnexus:start -->
-# GitNexus — Code Intelligence
+# GitNexus MCP
 
-This project is indexed by GitNexus as **GitNexus** (2273 symbols, 5419 relationships, 174 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+This project is indexed by GitNexus as **GitnexusV2** (1444 symbols, 3700 relationships, 111 execution flows).
 
-> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
+## Always Start Here
 
-## Always Do
+1. **Read `gitnexus://repo/{name}/context`** — codebase overview + check index freshness
+2. **Match your task to a skill below** and **read that skill file**
+3. **Follow the skill's workflow and checklist**
 
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
-- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
+> If step 1 warns the index is stale, run `npx gitnexus analyze` in the terminal first.
 
-## When Debugging
-
-1. `gitnexus_query({query: "<error or symptom>"})` — find execution flows related to the issue
-2. `gitnexus_context({name: "<suspect function>"})` — see all callers, callees, and process participation
-3. `READ gitnexus://repo/GitNexus/process/{processName}` — trace the full execution flow step by step
-4. For regressions: `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` — see what your branch changed
-
-## When Refactoring
-
-- **Renaming**: MUST use `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with `dry_run: false`.
-- **Extracting/Splitting**: MUST run `gitnexus_context({name: "target"})` to see all incoming/outgoing refs, then `gitnexus_impact({target: "target", direction: "upstream"})` to find all external callers before moving code.
-- After any refactor: run `gitnexus_detect_changes({scope: "all"})` to verify only expected files changed.
-
-## Never Do
-
-- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
-- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
-- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
-- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
-
-## Tools Quick Reference
-
-| Tool | When to use | Command |
-|------|-------------|---------|
-| `query` | Find code by concept | `gitnexus_query({query: "auth validation"})` |
-| `context` | 360-degree view of one symbol | `gitnexus_context({name: "validateUser"})` |
-| `impact` | Blast radius before editing | `gitnexus_impact({target: "X", direction: "upstream"})` |
-| `detect_changes` | Pre-commit scope check | `gitnexus_detect_changes({scope: "staged"})` |
-| `rename` | Safe multi-file rename | `gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true})` |
-| `cypher` | Custom graph queries | `gitnexus_cypher({query: "MATCH ..."})` |
-
-## Impact Risk Levels
-
-| Depth | Meaning | Action |
-|-------|---------|--------|
-| d=1 | WILL BREAK — direct callers/importers | MUST update these |
-| d=2 | LIKELY AFFECTED — indirect deps | Should test |
-| d=3 | MAY NEED TESTING — transitive | Test if critical path |
-
-## Resources
-
-| Resource | Use for |
-|----------|---------|
-| `gitnexus://repo/GitNexus/context` | Codebase overview, check index freshness |
-| `gitnexus://repo/GitNexus/clusters` | All functional areas |
-| `gitnexus://repo/GitNexus/processes` | All execution flows |
-| `gitnexus://repo/GitNexus/process/{name}` | Step-by-step execution trace |
-
-## Self-Check Before Finishing
-
-Before completing any code modification task, verify:
-1. `gitnexus_impact` was run for all modified symbols
-2. No HIGH/CRITICAL risk warnings were ignored
-3. `gitnexus_detect_changes()` confirms changes match expected scope
-4. All d=1 (WILL BREAK) dependents were updated
-
-## Keeping the Index Fresh
-
-After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
-
-```bash
-npx gitnexus analyze
-```
-
-If the index previously included embeddings, preserve them by adding `--embeddings`:
-
-```bash
-npx gitnexus analyze --embeddings
-```
-
-To check whether embeddings exist, inspect `.gitnexus/meta.json` — the `stats.embeddings` field shows the count (0 means no embeddings). **Running analyze without `--embeddings` will delete any previously generated embeddings.**
-
-> Claude Code users: A PostToolUse hook handles this automatically after `git commit` and `git merge`.
-
-## CLI
+## Skills
 
 | Task | Read this skill file |
 |------|---------------------|

README.md

@@ -34,7 +34,7 @@ https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72
 
 > *Like DeepWiki, but deeper.* DeepWiki helps you *understand* code. GitNexus lets you *analyze* it — because a knowledge graph tracks every relationship, not just descriptions.
 
-**TL;DR:** The **Web UI** is a quick way to chat with any repo. The **CLI + MCP** is how you make your AI agent actually reliable — it gives Cursor, Claude Code, Codex, and friends a deep architectural view of your codebase so they stop missing dependencies, breaking call chains, and shipping blind edits. Even smaller models get full architectural clarity, making it compete with goliath models.
+**TL;DR:** The **Web UI** is a quick way to chat with any repo. The **CLI + MCP** is how you make your AI agent actually reliable — it gives Cursor, Claude Code, and friends a deep architectural view of your codebase so they stop missing dependencies, breaking call chains, and shipping blind edits. Even smaller models get full architectural clarity, making it compete with goliath models.
 
 ---
 
@@ -48,10 +48,10 @@ https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72
 |                   | **CLI + MCP**                                            | **Web UI**                                             |
 | ----------------- | -------------------------------------------------------------- | ------------------------------------------------------------ |
 | **What**    | Index repos locally, connect AI agents via MCP                 | Visual graph explorer + AI chat in browser                   |
-| **For**     | Daily development with Cursor, Claude Code, Codex, Windsurf, OpenCode | Quick exploration, demos, one-off analysis                   |
+| **For**     | Daily development with Cursor, Claude Code, Windsurf, OpenCode | Quick exploration, demos, one-off analysis                   |
 | **Scale**   | Full repos, any size                                           | Limited by browser memory (~5k files), or unlimited via backend mode |
 | **Install** | `npm install -g gitnexus`                                    | No install —[gitnexus.vercel.app](https://gitnexus.vercel.app) |
-| **Storage** | LadybugDB native (fast, persistent)                               | LadybugDB WASM (in-memory, per session)                         |
+| **Storage** | KuzuDB native (fast, persistent)                               | KuzuDB WASM (in-memory, per session)                         |
 | **Parsing** | Tree-sitter native bindings                                    | Tree-sitter WASM                                             |
 | **Privacy** | Everything local, no network                                   | Everything in-browser, no server                             |
 
@@ -82,25 +82,18 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 
 | Editor                | MCP | Skills | Hooks (auto-augment) | Support        |
 | --------------------- | --- | ------ | -------------------- | -------------- |
-| **Claude Code** | Yes | Yes    | Yes (PreToolUse + PostToolUse) | **Full** |
+| **Claude Code** | Yes | Yes    | Yes (PreToolUse)     | **Full** |
 | **Cursor**      | Yes | Yes    | —                   | MCP + Skills   |
-| **Codex**       | Yes | Yes    | —                   | MCP + Skills   |
 | **Windsurf**    | Yes | —     | —                   | MCP            |
 | **OpenCode**    | Yes | Yes    | —                   | MCP + Skills   |
-| **Codex**       | Yes | —     | —                   | MCP            |
 
-> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that enrich searches with graph context + PostToolUse hooks that auto-reindex after commits.
+> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that automatically enrich grep/glob/bash calls with knowledge graph context.
 
-## Community Integrations
+### Community Integrations
 
-Built by the community — not officially maintained, but worth checking out.
-
-| Project | Author | Description |
-|---------|--------|-------------|
-| [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus) | [@tintinweb](https://github.com/tintinweb) | GitNexus plugin for [pi](https://pi.dev) — `pi install npm:pi-gitnexus` |
-| [gitnexus-stable-ops](https://github.com/ShunsukeHayashi/gitnexus-stable-ops) | [@ShunsukeHayashi](https://github.com/ShunsukeHayashi) | Stable ops & deployment workflows (Miyabi ecosystem) |
-
-> Have a project built on GitNexus? Open a PR to add it here!
+| Agent | Install | Source |
+|-------|---------|--------|
+| [pi](https://pi.dev) | `pi install npm:pi-gitnexus` | [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus) |
 
 If you prefer manual configuration:
 
@@ -110,12 +103,6 @@ If you prefer manual configuration:
 claude mcp add gitnexus -- npx -y gitnexus@latest mcp
 ```
 
-**Codex** (full support — MCP + skills):
-
-```bash
-codex mcp add gitnexus -- npx -y gitnexus@latest mcp
-```
-
 **Cursor** (`~/.cursor/mcp.json` — global, works for all projects):
 
 ```json
@@ -142,24 +129,13 @@ codex mcp add gitnexus -- npx -y gitnexus@latest mcp
 }
 ```
 
-**Codex** (`~/.codex/config.toml` for system scope, or `.codex/config.toml` for project scope):
-
-```toml
-[mcp_servers.gitnexus]
-command = "npx"
-args = ["-y", "gitnexus@latest", "mcp"]
-```
-
 ### CLI Commands
 
 ```bash
 gitnexus setup                    # Configure MCP for your editors (one-time)
 gitnexus analyze [path]           # Index a repository (or update stale index)
 gitnexus analyze --force          # Force full re-index
-gitnexus analyze --skills         # Generate repo-specific skill files from detected communities
 gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
-gitnexus analyze --embeddings     # Enable embedding generation (slower, better search)
-gitnexus analyze --verbose        # Log skipped files when parsers are unavailable
 gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
 gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
 gitnexus list                    # List all indexed repositories
@@ -213,10 +189,6 @@ gitnexus wiki --base-url <url>   # Wiki with custom LLM API base URL
 - **Impact Analysis** — Analyze blast radius before changes
 - **Refactoring** — Plan safe refactors using dependency mapping
 
-**Repo-specific skills** generated with `--skills`:
-
-When you run `gitnexus analyze --skills`, GitNexus detects the functional areas of your codebase (via Leiden community detection) and generates a `SKILL.md` file for each one under `.claude/skills/generated/`. Each skill describes a module's key files, entry points, execution flows, and cross-area connections — so your AI agent gets targeted context for the exact area of code you're working in. Skills are regenerated on each `--skills` run to stay current with the codebase.
-
 ---
 
 ## Multi-Repo MCP Architecture
@@ -245,8 +217,8 @@ flowchart TD
         Server["server.ts"]
         Backend["LocalBackend"]
         Pool["Connection Pool"]
-        ConnA["LadybugDB conn A"]
-        ConnB["LadybugDB conn B"]
+        ConnA["KuzuDB conn A"]
+        ConnB["KuzuDB conn B"]
     end
 
     Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
@@ -263,7 +235,7 @@ flowchart TD
     ConnB -->|"queries"| RepoB
 ```
 
-**How it works:** Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo (portable, gitignored) and registers a pointer in `~/.gitnexus/registry.json`. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the `repo` parameter is optional on all tools — agents don't need to change anything.
+**How it works:** Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo (portable, gitignored) and registers a pointer in `~/.gitnexus/registry.json`. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. KuzuDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the `repo` parameter is optional on all tools — agents don't need to change anything.
 
 ---
 
@@ -284,7 +256,7 @@ npm install
 npm run dev
 ```
 
-The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.
+The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, KuzuDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.
 
 **Local Backend Mode:** Run `gitnexus serve` and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.
 
@@ -292,7 +264,7 @@ The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAs
 
 ## The Problem GitNexus Solves
 
-Tools like **Cursor**, **Claude Code**, **Codex**, **Cline**, **Roo Code**, and **Windsurf** are powerful — but they don't truly know your codebase structure.
+Tools like **Cursor**, **Claude Code**, **Cline**, **Roo Code**, and **Windsurf** are powerful — but they don't truly know your codebase structure.
 
 **What happens:**
 
@@ -341,30 +313,14 @@ GitNexus builds a complete knowledge graph of your codebase through a multi-phas
 
 1. **Structure** — Walks the file tree and maps folder/file relationships
 2. **Parsing** — Extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
-3. **Resolution** — Resolves imports, function calls, heritage, constructor inference, and `self`/`this` receiver types across files with language-aware logic
+3. **Resolution** — Resolves imports and function calls across files with language-aware logic
 4. **Clustering** — Groups related symbols into functional communities
 5. **Processes** — Traces execution flows from entry points through call chains
 6. **Search** — Builds hybrid search indexes for fast retrieval
 
 ### Supported Languages
 
-| Language | Imports | Named Bindings | Exports | Heritage | Type Annotations | Constructor Inference | Config | Frameworks | Entry Points |
-|----------|---------|----------------|---------|----------|-----------------|---------------------|--------|------------|-------------|
-| TypeScript | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| JavaScript | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ |
-| Python | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Java | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| Kotlin | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| C# | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Go | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Rust | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| PHP | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Ruby | ✓ | — | ✓ | ✓ | — | ✓ | — | ✓ | ✓ |
-| Swift | — | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| C | — | — | ✓ | — | ✓ | ✓ | — | ✓ | ✓ |
-| C++ | — | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-
-**Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics
+TypeScript, JavaScript, Python, Java, Kotlin, C, C++, C#, Go, Rust, PHP, Swift
 
 ---
 
@@ -503,7 +459,7 @@ The wiki generator reads the indexed graph structure, groups files into modules
 | ------------------------- | ------------------------------------- | --------------------------------------- |
 | **Runtime**         | Node.js (native)                      | Browser (WASM)                          |
 | **Parsing**         | Tree-sitter native bindings           | Tree-sitter WASM                        |
-| **Database**        | LadybugDB native                         | LadybugDB WASM                             |
+| **Database**        | KuzuDB native                         | KuzuDB WASM                             |
 | **Embeddings**      | HuggingFace transformers.js (GPU/CPU) | transformers.js (WebGPU/WASM)           |
 | **Search**          | BM25 + semantic + RRF                 | BM25 + semantic + RRF                   |
 | **Agent Interface** | MCP (stdio)                           | LangChain ReAct agent                   |
@@ -524,10 +480,9 @@ The wiki generator reads the indexed graph structure, groups files into modules
 
 ### Recently Completed
 
-- [X] Constructor-Inferred Type Resolution, `self`/`this` Receiver Mapping
 - [X] Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
 - [X] Process-Grouped Search, 360-Degree Context, Claude Code Hooks
-- [X] Multi-Repo MCP, Zero-Config Setup, 13 Language Support
+- [X] Multi-Repo MCP, Zero-Config Setup, 11 Language Support
 - [X] Community Detection, Process Detection, Confidence Scoring
 - [X] Hybrid Search, Vector Index
 
@@ -544,7 +499,7 @@ The wiki generator reads the indexed graph structure, groups files into modules
 ## Acknowledgments
 
 - [Tree-sitter](https://tree-sitter.github.io/) — AST parsing
-- [LadybugDB](https://ladybugdb.com/) — Embedded graph database with vector support (formerly KuzuDB)
+- [KuzuDB](https://kuzudb.com/) — Embedded graph database with vector support
 - [Sigma.js](https://www.sigmajs.org/) — WebGL graph rendering
 - [transformers.js](https://huggingface.co/docs/transformers.js) — Browser ML
 - [Graphology](https://graphology.github.io/) — Graph data structures

compound-engineering.local.md

@@ -1,57 +0,0 @@
----
-review_agents: [kieran-typescript-reviewer, pattern-recognition-specialist, architecture-strategist, data-integrity-guardian, security-sentinel, performance-oracle, code-simplicity-reviewer]
-plan_review_agents: [kieran-typescript-reviewer, architecture-strategist, code-simplicity-reviewer]
-voltagent_agents: [voltagent-lang:typescript-pro, voltagent-qa-sec:security-auditor, voltagent-data-ai:database-optimizer]
----
-
-# Review Context
-
-## Project Overview
-GitNexus is a code intelligence tool that builds a knowledge graph from source code using tree-sitter AST parsing across 12 languages and KuzuDB for graph storage. Two packages: `gitnexus/` (CLI/MCP, TypeScript) and `gitnexus-web/` (browser).
-
-## Cross-Language Pattern Consistency (pattern-recognition-specialist)
-- 12 language-specific type extractors in `gitnexus/src/core/ingestion/type-extractors/` must follow identical patterns for: async unwrapping, constructor binding, namespace handling, nullable type stripping, for-loop element typing.
-- Past bugs: C#/Rust missing `await_expression` unwrapping that TypeScript handled correctly; PHP backslash namespace splitting inconsistent with other languages' `::` / `.` splitting.
-- When reviewing type extractor changes, verify the same pattern exists in ALL applicable language files — asymmetry is the #1 source of bugs.
-
-## Data Integrity (data-integrity-guardian)
-- KuzuDB graph operations: schema in `gitnexus/src/core/kuzu/schema.ts`, adapter in `kuzu-adapter.ts`.
-- The ingestion pipeline writes symbols and relationships to the graph — changes to node/relation schemas or the ingestion pipeline can corrupt the index.
-- Known issue: KuzuDB `close()` hangs on Linux due to C++ destructor — use `detachKuzu()` pattern.
-- `lbug-adapter.ts` fallback path needs quote/newline escaping for Cypher injection prevention.
-
-## Security (security-sentinel)
-- Cypher query construction in `lbug-adapter.ts` and `kuzu-adapter.ts` — watch for injection via unescaped user-provided symbol names.
-- CLI accepts `--repo` parameter and file paths — validate against path traversal.
-- MCP server exposes tools to external AI agents — all tool inputs are untrusted.
-
-## Performance (performance-oracle)
-- Tree-sitter buffer size is adaptive (512KB–32MB) via `getTreeSitterBufferSize()` in `constants.ts`.
-- The ingestion pipeline processes entire repositories — O(n) per file with potential O(n²) in cross-file resolution.
-- KuzuDB batch inserts vs individual inserts matter for large repos.
-
-## Architecture (architecture-strategist)
-- Ingestion pipeline phases: structure → parsing → imports → calls → heritage → processes → type resolution.
-- Shared modules: `export-detection.ts`, `constants.ts`, `utils.ts` — changes here have wide blast radius.
-- `gitnexus-web` package drifts behind CLI — flag if a change should be mirrored.
-
-## Voltagent Supplementary Agents
-
-Invoke these via the Agent tool alongside `/ce:review` for deeper specialist analysis. These cover gaps that compound-engineering agents don't:
-
-### voltagent-lang:typescript-pro
-**When:** Changes touch type-resolution logic, generics, conditional types, or complex type-level programming in `type-env.ts`, `type-extractors/*.ts`, or `types.ts`.
-**Why:** The type resolution system uses advanced TypeScript patterns (discriminated unions, mapped types, recursive generics) that benefit from deep TS type-system review beyond what kieran-typescript-reviewer covers.
-
-### voltagent-qa-sec:security-auditor
-**When:** Changes touch MCP tool handlers, Cypher query construction, CLI argument parsing, or any code that processes external input.
-**Why:** GitNexus is an MCP server — all tool inputs come from untrusted AI agents. Systematic OWASP-level audit catches injection vectors that spot-checking misses. Past finding: `lbug-adapter.ts` fallback path had unescaped newlines in Cypher queries.
-
-### voltagent-data-ai:database-optimizer
-**When:** Changes touch `kuzu-adapter.ts`, `schema.ts`, `lbug-adapter.ts`, or any Cypher query construction/execution.
-**Why:** No CE agent specializes in graph database optimization. KuzuDB batch insert patterns, index usage, and query planning directly affect analysis speed on large repos.
-
-## Review Tooling
-- Use `gitnexus_impact()` before approving changes to any symbol — check d=1 (WILL BREAK) callers.
-- Use `gitnexus_detect_changes({scope: "compare", base_ref: "main"})` to map PR diffs to affected execution flows.
-- Use claude-mem to surface past architectural decisions relevant to the code under review.

eval/README.md

@@ -148,7 +148,7 @@ Each mode has a `system_{mode}.jinja` + `instance_{mode}.jinja` pair. The agent
 
 1. Docker container starts with SWE-bench instance (repo at specific commit)
 2. **GitNexus setup**: Node.js + gitnexus installed, `gitnexus analyze` runs (or restores from cache)
-3. **Eval-server starts**: `gitnexus eval-server` daemon (persistent HTTP server, keeps LadybugDB warm)
+3. **Eval-server starts**: `gitnexus eval-server` daemon (persistent HTTP server, keeps KuzuDB warm)
 4. **Standalone tool scripts installed** in `/usr/local/bin/` — works with `subprocess.run` (no `.bashrc` needed)
 5. Agent runs with the configured model + system prompt + GitNexus tools
 6. Agent's patch is extracted as a git diff
@@ -167,7 +167,7 @@ Each tool script in `/usr/local/bin/` is standalone — no sourcing, no env inhe
 ### Eval-server
 
 The eval-server is a lightweight HTTP daemon that:
-- Keeps LadybugDB warm in memory (no cold start per tool call)
+- Keeps KuzuDB warm in memory (no cold start per tool call)
 - Returns LLM-friendly text (not raw JSON — saves tokens)
 - Includes next-step hints to guide tool chaining (query → context → impact → fix)
 - Auto-shuts down after idle timeout

eval/bridge/mcp_bridge.py

@@ -2,7 +2,7 @@
 MCP Bridge for GitNexus
 
 Starts the GitNexus MCP server as a subprocess and provides a Python interface
-to call MCP tools. Used by the bash wrapper scripts and the augmentation layer..
+to call MCP tools. Used by the bash wrapper scripts and the augmentation layer.
 
 The bridge communicates with the MCP server via stdio using the JSON-RPC protocol.
 """

eval/configs/models/deepseek-chat.yaml

@@ -1,13 +0,0 @@
-model: deepseek-ai/deepseek-chat
-provider: openrouter
-cost:
-  input: 0.14  # per 1M tokens
-  output: 0.28  # per 1M tokens
-  
-# Native DeepSeek API (direct)
-api_key: null
-base_url: null
-
-# For OpenRouter, uncomment below and comment out direct config above
-# api_key: \${OPENROUTER_API_KEY}
-# base_url: https://openrouter.ai/api/v1

eval/configs/models/deepseek-v3.yaml

@@ -1,15 +0,0 @@
-model: deepseek-ai/DeepSeek-V3
-provider: openrouter
-cost:
-  input: 0.27  # per 1M tokens
-  output: 1.10  # per 1M tokens
-  
-# Native DeepSeek API (direct)
-# Get your API key at: https://platform.deepseek.com/
-# Or use OpenRouter with: OPENROUTER_API_KEY
-api_key: null
-base_url: null
-
-# For OpenRouter, uncomment below and comment out direct config above
-# api_key: \${OPENROUTER_API_KEY}
-# base_url: https://openrouter.ai/api/v1

gitnexus-claude-plugin/hooks/gitnexus-hook.js

@@ -2,10 +2,8 @@
 /**
  * GitNexus Claude Code Plugin Hook
  *
- * PreToolUse  — intercepts Grep/Glob/Bash searches and augments
- *               with graph context from the GitNexus index.
- * PostToolUse — detects stale index after git mutations and notifies
- *               the agent to reindex.
+ * PreToolUse handler — intercepts Grep/Glob/Bash searches
+ * and augments with graph context from the GitNexus index.
  *
  * NOTE: SessionStart hooks are broken on Windows (Claude Code bug #23576).
  * Session context is injected via CLAUDE.md / skills instead.
@@ -28,19 +26,19 @@ function readInput() {
 }
 
 /**
- * Find the .gitnexus directory by walking up from startDir.
- * Returns the path to .gitnexus/ or null if not found.
+ * Check if a directory (or ancestor) has a .gitnexus index.
  */
-function findGitNexusDir(startDir) {
+function findGitNexusIndex(startDir) {
   let dir = startDir || process.cwd();
   for (let i = 0; i < 5; i++) {
-    const candidate = path.join(dir, '.gitnexus');
-    if (fs.existsSync(candidate)) return candidate;
+    if (fs.existsSync(path.join(dir, '.gitnexus'))) {
+      return true;
+    }
     const parent = path.dirname(dir);
     if (parent === dir) break;
     dir = parent;
   }
-  return null;
+  return false;
 }
 
 /**
@@ -85,146 +83,66 @@ function extractPattern(toolName, toolInput) {
   return null;
 }
 
-/**
- * Spawn a gitnexus CLI command synchronously.
- * Detects binary on PATH once, then runs exactly once.
- *
- * SECURITY: Never use shell: true with user-controlled arguments.
- * On Windows, invoke gitnexus.cmd directly (no shell needed).
- */
-function runGitNexusCli(args, cwd, timeout) {
-  const isWin = process.platform === 'win32';
-
-  // Detect whether 'gitnexus' is on PATH (cheap check, no execution)
-  let useDirectBinary = false;
-  try {
-    const which = spawnSync(
-      isWin ? 'where' : 'which', ['gitnexus'],
-      { encoding: 'utf-8', timeout: 3000, stdio: ['pipe', 'pipe', 'pipe'] }
-    );
-    useDirectBinary = which.status === 0;
-  } catch { /* not on PATH */ }
-
-  if (useDirectBinary) {
-    return spawnSync(
-      isWin ? 'gitnexus.cmd' : 'gitnexus', args,
-      { encoding: 'utf-8', timeout, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
-    );
-  }
-  // npx fallback needs shell on Windows since npx is a .cmd script
-  return spawnSync(
-    isWin ? 'npx.cmd' : 'npx', ['-y', 'gitnexus', ...args],
-    { encoding: 'utf-8', timeout: timeout + 5000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
-  );
-}
-
-/**
- * Emit a hook response with additional context for the agent.
- */
-function sendHookResponse(hookEventName, message) {
-  console.log(JSON.stringify({
-    hookSpecificOutput: { hookEventName, additionalContext: message }
-  }));
-}
-
-/**
- * PreToolUse handler — augment searches with graph context.
- */
-function handlePreToolUse(input) {
-  const cwd = input.cwd || process.cwd();
-  if (!path.isAbsolute(cwd)) return;
-  if (!findGitNexusDir(cwd)) return;
-
-  const toolName = input.tool_name || '';
-  const toolInput = input.tool_input || {};
-
-  if (toolName !== 'Grep' && toolName !== 'Glob' && toolName !== 'Bash') return;
-
-  const pattern = extractPattern(toolName, toolInput);
-  if (!pattern || pattern.length < 3) return;
-
-  let result = '';
-  try {
-    const child = runGitNexusCli(['augment', '--', pattern], cwd, 7000);
-    if (!child.error && child.status === 0) {
-      result = child.stderr || '';
-    }
-  } catch { /* graceful failure */ }
-
-  if (result && result.trim()) {
-    sendHookResponse('PreToolUse', result.trim());
-  }
-}
-
-/**
- * PostToolUse handler — detect index staleness after git mutations.
- *
- * Instead of spawning a full `gitnexus analyze` synchronously (which blocks
- * the agent for up to 120s and risks LadybugDB corruption on timeout), we do a
- * lightweight staleness check: compare `git rev-parse HEAD` against the
- * lastCommit stored in `.gitnexus/meta.json`. If they differ, notify the
- * agent so it can decide when to reindex.
- */
-function handlePostToolUse(input) {
-  const toolName = input.tool_name || '';
-  if (toolName !== 'Bash') return;
-
-  const command = (input.tool_input || {}).command || '';
-  if (!/\bgit\s+(commit|merge|rebase|cherry-pick|pull)(\s|$)/.test(command)) return;
-
-  // Only proceed if the command succeeded
-  const toolOutput = input.tool_output || {};
-  if (toolOutput.exit_code !== undefined && toolOutput.exit_code !== 0) return;
-
-  const cwd = input.cwd || process.cwd();
-  if (!path.isAbsolute(cwd)) return;
-  const gitNexusDir = findGitNexusDir(cwd);
-  if (!gitNexusDir) return;
-
-  // Compare HEAD against last indexed commit — skip if unchanged
-  let currentHead = '';
-  try {
-    const headResult = spawnSync('git', ['rev-parse', 'HEAD'], {
-      encoding: 'utf-8', timeout: 3000, cwd, stdio: ['pipe', 'pipe', 'pipe'],
-    });
-    currentHead = (headResult.stdout || '').trim();
-  } catch { return; }
-
-  if (!currentHead) return;
-
-  let lastCommit = '';
-  let hadEmbeddings = false;
-  try {
-    const meta = JSON.parse(fs.readFileSync(path.join(gitNexusDir, 'meta.json'), 'utf-8'));
-    lastCommit = meta.lastCommit || '';
-    hadEmbeddings = (meta.stats && meta.stats.embeddings > 0);
-  } catch { /* no meta — treat as stale */ }
-
-  // If HEAD matches last indexed commit, no reindex needed
-  if (currentHead && currentHead === lastCommit) return;
-
-  const analyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
-  sendHookResponse('PostToolUse',
-    `GitNexus index is stale (last indexed: ${lastCommit ? lastCommit.slice(0, 7) : 'never'}). ` +
-    `Run \`${analyzeCmd}\` to update the knowledge graph.`
-  );
-}
-
-// Dispatch map for hook events
-const handlers = {
-  PreToolUse: handlePreToolUse,
-  PostToolUse: handlePostToolUse,
-};
-
 function main() {
   try {
     const input = readInput();
-    const handler = handlers[input.hook_event_name || ''];
-    if (handler) handler(input);
-  } catch (err) {
-    if (process.env.GITNEXUS_DEBUG) {
-      console.error('GitNexus hook error:', (err.message || '').slice(0, 200));
+    const hookEvent = input.hook_event_name || '';
+
+    if (hookEvent !== 'PreToolUse') return;
+
+    const cwd = input.cwd || process.cwd();
+    if (!findGitNexusIndex(cwd)) return;
+
+    const toolName = input.tool_name || '';
+    const toolInput = input.tool_input || {};
+
+    if (toolName !== 'Grep' && toolName !== 'Glob' && toolName !== 'Bash') return;
+
+    const pattern = extractPattern(toolName, toolInput);
+    if (!pattern || pattern.length < 3) return;
+
+    // augment CLI writes result to stderr (KuzuDB's native module captures
+    // stdout fd at OS level, making it unusable in subprocess contexts).
+    let result = '';
+
+    const isWin = process.platform === 'win32';
+
+    // Try direct gitnexus binary first (faster if globally installed)
+    try {
+      const child = spawnSync(
+        'gitnexus',
+        ['augment', pattern],
+        { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'], shell: isWin }
+      );
+      if (child.status === 0 && child.stderr && child.stderr.trim()) {
+        result = child.stderr;
+      }
+    } catch { /* not on PATH */ }
+
+    // Fallback to npx if direct binary didn't produce output
+    if (!result || !result.trim()) {
+      try {
+        const child = spawnSync(
+          'npx',
+          ['-y', 'gitnexus', 'augment', pattern],
+          { encoding: 'utf-8', timeout: 15000, cwd, stdio: ['pipe', 'pipe', 'pipe'], shell: isWin }
+        );
+        if (child.status === 0 && child.stderr && child.stderr.trim()) {
+          result = child.stderr;
+        }
+      } catch { /* graceful failure */ }
     }
+
+    if (result && result.trim()) {
+      console.log(JSON.stringify({
+        hookSpecificOutput: {
+          hookEventName: 'PreToolUse',
+          additionalContext: result.trim()
+        }
+      }));
+    }
+  } catch {
+    // Graceful failure
   }
 }
 

gitnexus-claude-plugin/hooks/hooks.json

@@ -12,19 +12,6 @@
           }
         ]
       }
-    ],
-    "PostToolUse": [
-      {
-        "matcher": "Bash",
-        "hooks": [
-          {
-            "type": "command",
-            "command": "node ${CLAUDE_PLUGIN_ROOT}/hooks/gitnexus-hook.js",
-            "timeout": 10,
-            "statusMessage": "Checking GitNexus index freshness..."
-          }
-        ]
-      }
     ]
   }
 }

gitnexus-web/package.json

@@ -6,8 +6,7 @@
   "scripts": {
     "dev": "vite",
     "build": "tsc -b && vite build",
-    "preview": "vite preview",
-    "test": "vitest run"
+    "preview": "vite preview"
   },
   "dependencies": {
     "@huggingface/transformers": "^3.0.0",
@@ -34,7 +33,7 @@
     "graphology-layout-noverlap": "^0.4.2",
     "isomorphic-git": "^1.36.1",
     "jszip": "^3.10.1",
-    "@ladybugdb/wasm-core": "^0.15.2",
+    "kuzu-wasm": "^0.11.1",
     "langchain": "^1.2.10",
     "lru-cache": "^11.2.4",
     "lucide-react": "^0.562.0",
@@ -66,7 +65,6 @@
     "tree-sitter-wasms": "^0.1.13",
     "typescript": "^5.4.5",
     "vite": "^5.2.0",
-    "vite-plugin-static-copy": "^3.1.4",
-    "vitest": "^4.0.18"
+    "vite-plugin-static-copy": "^3.1.4"
   }
 }

gitnexus-web/src/App.tsx

@@ -13,7 +13,6 @@ import { FileEntry } from './services/zip';
 import { getActiveProviderConfig } from './core/llm/settings-service';
 import { createKnowledgeGraph } from './core/graph/graph';
 import { connectToServer, fetchRepos, normalizeServerUrl, type ConnectToServerResult } from './services/server-connection';
-import { HelpPanel } from './components/HelpPanel';
 
 const AppContent = () => {
   const {
@@ -29,8 +28,6 @@ const AppContent = () => {
     runPipelineFromFiles,
     isSettingsPanelOpen,
     setSettingsPanelOpen,
-    isHelpDialogBoxOpen,
-    setHelpDialogBoxOpen,
     refreshLLMSettings,
     initializeAgent,
     startEmbeddings,
@@ -43,8 +40,6 @@ const AppContent = () => {
     availableRepos,
     setAvailableRepos,
     switchRepo,
-    loadServerGraph,
-    graph
   } = useAppState();
 
   const graphCanvasRef = useRef<GraphCanvasHandle>(null);
@@ -137,13 +132,13 @@ const AppContent = () => {
     }
   }, [setViewMode, setGraph, setFileContents, setProgress, setProjectName, runPipelineFromFiles, startEmbeddings, initializeAgent]);
 
-  const handleServerConnect = useCallback((result: ConnectToServerResult): Promise<void> => {
+  const handleServerConnect = useCallback((result: ConnectToServerResult) => {
     // Extract project name from repoPath
     const repoPath = result.repoInfo.repoPath;
     const projectName = repoPath.split('/').pop() || 'server-project';
     setProjectName(projectName);
 
-    // Build KnowledgeGraph from server data for visualization
+    // Build KnowledgeGraph from server data (bypasses WASM pipeline entirely)
     const graph = createKnowledgeGraph();
     for (const node of result.nodes) {
       graph.addNode(node);
@@ -163,30 +158,20 @@ const AppContent = () => {
     // Transition directly to exploring view
     setViewMode('exploring');
 
-    // Load graph into LadybugDB (in-browser WASM database) for Nexus AI queries,
-    // then initialize agent once the database is ready
-    const loadGraphPromise = loadServerGraph(result.nodes, result.relationships, result.fileContents)
-      .then(() => {
-        if (getActiveProviderConfig()) {
-          return initializeAgent(projectName);
-        }
-      })
-      .then(() => {
-        startEmbeddings().catch((err) => {
-          if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
-            startEmbeddings('wasm').catch(console.warn);
-          } else {
-            console.warn('Embeddings auto-start failed:', err);
-          }
-        });
-      })
-      .catch((err) => {
-        console.warn('Failed to load graph into LadybugDB:', err);
-        // Agent won't work but graph visualization still does
-      });
+    // Initialize agent if LLM is configured
+    if (getActiveProviderConfig()) {
+      initializeAgent(projectName);
+    }
 
-    return loadGraphPromise;
-  }, [setViewMode, setGraph, setFileContents, setProjectName, loadServerGraph, initializeAgent, startEmbeddings]);
+    // Auto-start embeddings
+    startEmbeddings().catch((err) => {
+      if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
+        startEmbeddings('wasm').catch(console.warn);
+      } else {
+        console.warn('Embeddings auto-start failed:', err);
+      }
+    });
+  }, [setViewMode, setGraph, setFileContents, setProjectName, initializeAgent, startEmbeddings]);
 
   // Auto-connect when ?server query param is present (bookmarkable shortcut)
   const autoConnectRan = useRef(false);
@@ -218,12 +203,16 @@ const AppContent = () => {
         setProgress({ phase: 'extracting', percent: 97, message: 'Processing...', detail: 'Extracting file contents' });
       }
     }).then(async (result) => {
-      await handleServerConnect(result);
-      setProgress(null);
+      handleServerConnect(result);
+
+      // Store server URL and fetch available repos for the repo switcher
       setServerBaseUrl(baseUrl);
-      fetchRepos(baseUrl)
-        .then((repos) => setAvailableRepos(repos))
-        .catch((e) => console.warn('Failed to fetch repo list:', e));
+      try {
+        const repos = await fetchRepos(baseUrl);
+        setAvailableRepos(repos);
+      } catch (e) {
+        console.warn('Failed to fetch repo list:', e);
+      }
     }).catch((err) => {
       console.error('Auto-connect failed:', err);
       setProgress({
@@ -257,14 +246,16 @@ const AppContent = () => {
         onFileSelect={handleFileSelect}
         onGitClone={handleGitClone}
         onServerConnect={async (result, serverUrl) => {
-          await handleServerConnect(result);
-          setProgress(null);
+          handleServerConnect(result);
           if (serverUrl) {
             const baseUrl = normalizeServerUrl(serverUrl);
             setServerBaseUrl(baseUrl);
-            fetchRepos(baseUrl)
-              .then((repos) => setAvailableRepos(repos))
-              .catch((e) => console.warn('Failed to fetch repo list:', e));
+            try {
+              const repos = await fetchRepos(baseUrl);
+              setAvailableRepos(repos);
+            } catch (e) {
+              console.warn('Failed to fetch repo list:', e);
+            }
           }
         }}
       />
@@ -309,13 +300,6 @@ const AppContent = () => {
         onSettingsSaved={handleSettingsSaved}
       />
 
-      <HelpPanel
-          isOpen={isHelpDialogBoxOpen}
-          onClose={() => setHelpDialogBoxOpen(false)}
-          nodeCount={graph!.nodes.length}
-          edgeCount={graph!.relationships.length}
-      />
-
     </div>
   );
 };

gitnexus-web/src/components/CodeReferencesPanel.tsx

@@ -5,42 +5,6 @@ import { vscDarkPlus } from 'react-syntax-highlighter/dist/esm/styles/prism';
 import { useAppState } from '../hooks/useAppState';
 import { NODE_COLORS } from '../lib/constants';
 
-/** Map file extension to Prism syntax highlighter language identifier */
-const getSyntaxLanguage = (filePath: string | undefined): string => {
-  if (!filePath) return 'text';
-  const ext = filePath.split('.').pop()?.toLowerCase();
-  switch (ext) {
-    case 'js': case 'jsx': case 'mjs': case 'cjs': return 'javascript';
-    case 'ts': case 'tsx': case 'mts': case 'cts': return 'typescript';
-    case 'py': case 'pyw': return 'python';
-    case 'rb': case 'rake': case 'gemspec': return 'ruby';
-    case 'java': return 'java';
-    case 'go': return 'go';
-    case 'rs': return 'rust';
-    case 'c': case 'h': return 'c';
-    case 'cpp': case 'cc': case 'cxx': case 'hpp': case 'hxx': case 'hh': return 'cpp';
-    case 'cs': return 'csharp';
-    case 'php': return 'php';
-    case 'kt': case 'kts': return 'kotlin';
-    case 'swift': return 'swift';
-    case 'json': return 'json';
-    case 'yaml': case 'yml': return 'yaml';
-    case 'md': case 'mdx': return 'markdown';
-    case 'html': case 'htm': case 'erb': return 'markup';
-    case 'css': case 'scss': case 'sass': return 'css';
-    case 'sh': case 'bash': case 'zsh': return 'bash';
-    case 'sql': return 'sql';
-    case 'xml': return 'xml';
-    default: break;
-  }
-  // Handle extensionless Ruby files
-  const basename = filePath.split('/').pop() || '';
-  if (['Rakefile', 'Gemfile', 'Guardfile', 'Vagrantfile', 'Brewfile'].includes(basename)) return 'ruby';
-  if (['Makefile'].includes(basename)) return 'makefile';
-  if (['Dockerfile'].includes(basename)) return 'docker';
-  return 'text';
-};
-
 // Match the code theme used elsewhere in the app
 const customTheme = {
   ...vscDarkPlus,
@@ -303,7 +267,12 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
             <div className="flex-1 min-h-0 overflow-auto scrollbar-thin">
               {selectedFileContent ? (
                 <SyntaxHighlighter
-                  language={getSyntaxLanguage(selectedFilePath)}
+                  language={
+                    selectedFilePath?.endsWith('.py') ? 'python' :
+                    selectedFilePath?.endsWith('.js') || selectedFilePath?.endsWith('.jsx') ? 'javascript' :
+                    selectedFilePath?.endsWith('.ts') || selectedFilePath?.endsWith('.tsx') ? 'typescript' :
+                    'text'
+                  }
                   style={customTheme as any}
                   showLineNumbers
                   startingLineNumber={1}
@@ -370,7 +339,11 @@ export const CodeReferencesPanel = ({ onFocusNode }: CodeReferencesPanelProps) =
           const hasRange = typeof ref.startLine === 'number';
           const startDisplay = hasRange ? (ref.startLine ?? 0) + 1 : undefined;
           const endDisplay = hasRange ? (ref.endLine ?? ref.startLine ?? 0) + 1 : undefined;
-          const language = getSyntaxLanguage(ref.filePath);
+          const language =
+            ref.filePath.endsWith('.py') ? 'python' :
+            ref.filePath.endsWith('.js') || ref.filePath.endsWith('.jsx') ? 'javascript' :
+            ref.filePath.endsWith('.ts') || ref.filePath.endsWith('.tsx') ? 'typescript' :
+            'text';
 
           const isGlowing = glowRefId === ref.id;
 

gitnexus-web/src/components/EmbeddingStatus.tsx

@@ -83,7 +83,7 @@ export const EmbeddingStatus = () => {
             <button
               onClick={handleTestArrayParams}
               className="flex items-center gap-1 px-2 py-1.5 bg-surface border border-border-subtle rounded-lg text-xs text-text-muted hover:bg-hover hover:text-text-secondary transition-all"
-              title="Test if LadybugDB supports array params"
+              title="Test if KuzuDB supports array params"
             >
               <FlaskConical className="w-3 h-3" />
               {testResult || 'Test'}

gitnexus-web/src/components/GraphCanvas.tsx

@@ -26,9 +26,6 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
     blastRadiusNodeIds,
     isAIHighlightsEnabled,
     toggleAIHighlights,
-    clearAIToolHighlights,
-    clearAICitationHighlights,
-    clearBlastRadius,
     animatedNodes,
   } = useAppState();
   const [hoveredNodeName, setHoveredNodeName] = useState<string | null>(null);
@@ -308,13 +305,9 @@ export const GraphCanvas = forwardRef<GraphCanvasHandle>((_, ref) => {
       <div className="absolute top-4 right-4 z-20">
         <button
           onClick={() => {
+            // If turning off, also clear process highlights
             if (isAIHighlightsEnabled) {
-              // Turning off — clear AI highlights and selection (preserve user query highlights)
-              clearAIToolHighlights();
-              clearAICitationHighlights();
-              clearBlastRadius();
-              setSelectedNode(null);
-              setSigmaSelectedNode(null);
+              setHighlightedNodeIds(new Set());
             }
             toggleAIHighlights();
           }}

gitnexus-web/src/components/Header.tsx

@@ -32,7 +32,6 @@ export const Header = ({ onFocusNode, availableRepos = [], onSwitchRepo }: Heade
     isRightPanelOpen,
     rightPanelTab,
     setSettingsPanelOpen,
-    setHelpDialogBoxOpen
   } = useAppState();
   const [isRepoDropdownOpen, setIsRepoDropdownOpen] = useState(false);
   const repoDropdownRef = useRef<HTMLDivElement>(null);
@@ -267,13 +266,10 @@ export const Header = ({ onFocusNode, availableRepos = [], onSwitchRepo }: Heade
           className="w-9 h-9 flex items-center justify-center rounded-md text-text-secondary hover:bg-hover hover:text-text-primary transition-colors"
           title="AI Settings"
         >
-          <Settings className="w-4.5 h-4.5" />
+          <Settings className="w-[18px] h-[18px]" />
         </button>
-        <button
-          title="Help"
-          onClick={() => setHelpDialogBoxOpen(true)}
-          className="w-9 h-9 flex items-center justify-center rounded-md text-text-secondary hover:bg-hover hover:text-text-primary transition-colors">
-          <HelpCircle className="w-4.5 h-4.5" />
+        <button className="w-9 h-9 flex items-center justify-center rounded-md text-text-secondary hover:bg-hover hover:text-text-primary transition-colors">
+          <HelpCircle className="w-[18px] h-[18px]" />
         </button>
 
         {/* AI Button */}

gitnexus-web/src/components/HelpPanel.tsx

@@ -1,390 +0,0 @@
-import React, { useState } from 'react';
-import { X, GitBranch, Search, Filter, Zap, Keyboard, BarChart2, HelpCircle } from 'lucide-react';
-
-interface HelpPanelProps {
-    isOpen: boolean;
-    onClose: () => void;
-    nodeCount: number;
-    edgeCount: number;
-}
-
-type TabId = 'overview' | 'graph' | 'search' | 'ai' | 'shortcuts' | 'status';
-
-interface Tab {
-    id: TabId;
-    label: string;
-    icon: React.ReactNode;
-}
-
-const tabs: Tab[] = [
-    { id: 'overview',  label: 'Overview',        icon: <HelpCircle className="w-4 h-4" /> },
-    { id: 'graph',     label: 'Graph & nodes',   icon: <GitBranch className="w-4 h-4" /> },
-    { id: 'search',    label: 'Search & filter', icon: <Search className="w-4 h-4" /> },
-    { id: 'ai',        label: 'Nexus AI',         icon: <Zap className="w-4 h-4" /> },
-    { id: 'shortcuts', label: 'Shortcuts',        icon: <Keyboard className="w-4 h-4" /> },
-    { id: 'status',    label: 'Status bar',       icon: <BarChart2 className="w-4 h-4" /> },
-];
-
-const shortcuts = [
-    { label: 'Search nodes',      mac: '⌘ K',  win: 'Ctrl K' },
-    { label: 'Deselect / close',  mac: 'Esc',   win: 'Esc'    },
-];
-
-const nodeColors = [
-    { color: '#10b981', label: 'Function',   desc: 'Function declarations' },
-    { color: '#3b82f6', label: 'File',        desc: 'Source files' },
-    { color: '#f59e0b', label: 'Class',       desc: 'Class declarations' },
-    { color: '#14b8a6', label: 'Method',      desc: 'Class methods' },
-    { color: '#ec4899', label: 'Interface',   desc: 'TypeScript interfaces' },
-    { color: '#6366f1', label: 'Folder',      desc: 'Directory nodes' },
-];
-
-const getStatusItems = (nodeCount: number, edgeCount: number) => [
-    { badge: <span style={{ width: 8, height: 8, borderRadius: '50%', background: '#34d399', display: 'inline-block', flexShrink: 0 }} />, title: 'Ready', desc: 'Graph is fully loaded and interactive' },
-    { badge: <span style={{ fontSize: 12, fontWeight: 500, color: '#a78bfa', flexShrink: 0 }}>{nodeCount}</span>, title: 'Nodes count', desc: 'Total files and symbols in the graph' },
-    { badge: <span style={{ fontSize: 12, fontWeight: 500, color: '#60a5fa', flexShrink: 0 }}>{edgeCount}</span>, title: 'Edges count', desc: 'Import / dependency connections' },
-    { badge: <span style={{ fontSize: 11, fontWeight: 500, color: '#34d399', flexShrink: 0, whiteSpace: 'nowrap' }}>Semantic Ready</span>, title: 'AI index status', desc: 'Repo is fully indexed for AI queries' },
-    // { badge: <span style={{ fontSize: 11, fontWeight: 500, color: '#9ca3af', flexShrink: 0 }}>typescript</span>, title: 'Language', desc: 'Primary language detected in the repo' },
-];
-
-const kbdStyle: React.CSSProperties = {
-    fontSize: 11,
-    background: 'rgba(255,255,255,0.08)',
-    borderRadius: 4,
-    padding: '2px 8px',
-    color: '#e2e2e8',
-    fontFamily: 'monospace',
-    border: '0.5px solid rgba(255,255,255,0.12)',
-    whiteSpace: 'nowrap',
-};
-
-const kbdWinStyle: React.CSSProperties = {
-    ...kbdStyle,
-    color: '#93c5fd',
-};
-
-function TabContent({ active, nodeCount, edgeCount }: {
-    active: TabId;
-    nodeCount: number;
-    edgeCount: number;
-}) {
-    if (active === 'overview') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 10 }}>
-            <p style={{ fontSize: 11, color: '#6b7280', margin: '0 0 4px', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Getting started</p>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px', borderLeft: '2px solid #a78bfa' }}>
-                <p style={{ fontSize: 13, fontWeight: 500, color: '#e2e2e8', margin: '0 0 4px' }}>What is GitNexus?</p>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>An interactive graph explorer for your codebase. Every file, function, and import becomes a node you can explore, query, and navigate visually.</p>
-            </div>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px', borderLeft: '2px solid #34d399' }}>
-                <p style={{ fontSize: 13, fontWeight: 500, color: '#e2e2e8', margin: '0 0 4px' }}>Your current repo</p>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    Loaded: <span style={{ color: '#a78bfa', fontFamily: 'monospace' }}></span>  {nodeCount} nodes · {edgeCount} edges
-                </p>
-            </div>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px', borderLeft: '2px solid #60a5fa' }}>
-                <p style={{ fontSize: 13, fontWeight: 500, color: '#e2e2e8', margin: '0 0 4px' }}>Three ways to explore</p>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    <strong style={{ color: '#e2e2e8', fontWeight: 500 }}>1.</strong> Click nodes to inspect
-                    <br/>
-                    <strong style={{ color: '#e2e2e8', fontWeight: 500 }}>2.</strong> Search by name or type
-                    <br/>
-                    <strong style={{ color: '#e2e2e8', fontWeight: 500 }}>3.</strong> Ask Nexus AI a natural language question
-                </p>
-            </div>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px', borderLeft: '2px solid #fbbf24' }}>
-                <p style={{ fontSize: 13, fontWeight: 500, color: '#e2e2e8', margin: '0 0 4px' }}>Navigation</p>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    · Scroll to zoom <br/>
-                    · Click and drag to pan <br/>
-                    · Double-click a node to focus its subgraph
-                </p>
-            </div>
-        </div>
-    );
-
-    if (active === 'graph') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 12 }}>
-            <p style={{ fontSize: 11, color: '#6b7280', margin: '0 0 4px', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Node color legend</p>
-
-            {nodeColors.map(({ color, label, desc }) => (
-                <div key={label} style={{ display: 'flex', gap: 10, alignItems: 'flex-start' }}>
-                    <span style={{ width: 12, height: 12, borderRadius: '50%', background: color, flexShrink: 0, marginTop: 2 }} />
-                    <div>
-                        <p style={{ fontSize: 12, fontWeight: 500, color: '#e2e2e8', margin: '0 0 2px' }}>{label} nodes</p>
-                        <p style={{ fontSize: 12, color: '#9ca3af', margin: 0 }}>{desc}</p>
-                    </div>
-                </div>
-            ))}
-
-            <div style={{ borderTop: '0.5px solid rgba(255,255,255,0.08)', margin: '4px 0' }} />
-
-            <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                Node <strong style={{ color: '#e2e2e8', fontWeight: 500 }}>size</strong> reflects connection count — larger nodes are depended on by more files. Edges point from importer → imported.
-            </p>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '10px 14px' }}>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    Click any node to open its detail panel — showing imports, exports, and reverse dependencies.
-                </p>
-            </div>
-        </div>
-    );
-
-    if (active === 'search') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 10 }}>
-            <p style={{ fontSize: 11, color: '#6b7280', margin: '0 0 4px', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Search & filter</p>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px' }}>
-                <div style={{ display: 'flex', alignItems: 'center', gap: 8, marginBottom: 6 }}>
-                    <kbd style={kbdStyle}>⌘K</kbd>/
-                    <kbd style={kbdStyle}>Ctrl K</kbd>
-                    <p style={{ fontSize: 12, fontWeight: 500, color: '#e2e2e8', margin: 0 }}>Search nodes</p>
-                </div>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    Search by filename, function name, or import path. Matching nodes are highlighted live in the graph.
-                </p>
-            </div>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px' }}>
-                <div style={{ display: 'flex', alignItems: 'center', gap: 8, marginBottom: 6 }}>
-                    <Filter style={{ width: 14, height: 14, color: '#a78bfa', flexShrink: 0 }} />
-                    <p style={{ fontSize: 12, fontWeight: 500, color: '#e2e2e8', margin: 0 }}>Filter panel</p>
-                </div>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    Use the filter icon in the left sidebar to isolate specific node types, hide leaf nodes, or focus on a depth range from a selected root.
-                </p>
-            </div>
-
-            <div style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '12px 14px' }}>
-                <p style={{ fontSize: 12, fontWeight: 500, color: '#e2e2e8', margin: '0 0 6px' }}>Search syntax</p>
-                {[
-                    { query: 'auth',        hint: 'match by name fragment' },
-                    { query: './utils/',    hint: 'match by path prefix' },
-                    { query: 'type:config', hint: 'filter by node type' },
-                ].map(({ query, hint }) => (
-                    <div key={query} style={{ display: 'flex', alignItems: 'baseline', gap: 8, marginBottom: 4 }}>
-                        <code style={{ fontSize: 11, color: '#a78bfa', background: 'rgba(167,139,250,0.1)', borderRadius: 4, padding: '1px 6px', fontFamily: 'monospace', flexShrink: 0 }}>{query}</code>
-                        <span style={{ fontSize: 12, color: '#6b7280' }}>{hint}</span>
-                    </div>
-                ))}
-            </div>
-        </div>
-    );
-
-    if (active === 'ai') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 10 }}>
-            <p style={{ fontSize: 11, color: '#6b7280', margin: '0 0 4px', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Nexus AI</p>
-
-            <div style={{ background: 'rgba(167,139,250,0.08)', border: '0.5px solid rgba(167,139,250,0.25)', borderRadius: 10, padding: '12px 14px' }}>
-                <p style={{ fontSize: 12, fontWeight: 500, color: '#a78bfa', margin: '0 0 4px' }}>✓ Semantic Ready</p>
-                <p style={{ fontSize: 12, color: '#9ca3af', margin: 0, lineHeight: 1.6 }}>
-                    Your repo is indexed and ready for semantic queries. Nexus AI understands code structure and relationships, not just file names.
-                </p>
-            </div>
-
-            <p style={{ fontSize: 12, color: '#9ca3af', margin: '4px 0 2px' }}>Try asking:</p>
-            {[
-                '"Which files depend on the auth module?"',
-                '"Find circular dependencies in this repo"',
-                '"What are the most connected components?"',
-                '"Show me all files that import useEffect"',
-            ].map(q => (
-                <div key={q} style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 8, padding: '8px 12px', fontSize: 12, color: '#e2e2e8', fontStyle: 'italic' }}>{q}</div>
-            ))}
-
-            <div style={{ borderTop: '0.5px solid rgba(255,255,255,0.08)', margin: '4px 0' }} />
-
-            <p style={{ fontSize: 12, color: '#6b7280', margin: 0, lineHeight: 1.6 }}>
-                Open the prompt via  the{' '}
-                <span style={{ color: '#e2e2e8' }}>Nexus AI</span> button (top-right).
-            </p>
-        </div>
-    );
-
-    if (active === 'shortcuts') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 0 }}>
-            {/* Column headers */}
-            <div style={{
-                display: 'grid',
-                gridTemplateColumns: '1fr 80px 88px',
-                gap: 8,
-                padding: '0 0 8px',
-                borderBottom: '0.5px solid rgba(255,255,255,0.08)',
-                marginBottom: 4,
-            }}>
-                <span style={{ fontSize: 11, color: '#6b7280', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Action</span>
-                <span style={{ fontSize: 11, color: '#6b7280', textTransform: 'uppercase', letterSpacing: '0.08em', textAlign: 'center' }}>Mac</span>
-                <span style={{ fontSize: 11, color: '#93c5fd', textTransform: 'uppercase', letterSpacing: '0.08em', textAlign: 'center' }}>Windows</span>
-            </div>
-
-            {shortcuts.map(({ label, mac, win }, i) => (
-                <div
-                    key={label}
-                    style={{
-                        display: 'grid',
-                        gridTemplateColumns: '1fr 80px 88px',
-                        gap: 8,
-                        alignItems: 'center',
-                        padding: '8px 0',
-                        borderBottom: i < shortcuts.length - 1 ? '0.5px solid rgba(255,255,255,0.05)' : 'none',
-                    }}
-                >
-                    <span style={{ fontSize: 12, color: '#9ca3af' }}>{label}</span>
-                    <span style={{ display: 'flex', justifyContent: 'center' }}>
-                        <kbd style={kbdStyle}>{mac}</kbd>
-                    </span>
-                    <span style={{ display: 'flex', justifyContent: 'center' }}>
-                        <kbd style={kbdWinStyle}>{win}</kbd>
-                    </span>
-                </div>
-            ))}
-        </div>
-    );
-
-    if (active === 'status') return (
-        <div style={{ display: 'flex', flexDirection: 'column', gap: 8 }}>
-            <p style={{ fontSize: 11, color: '#6b7280', margin: '0 0 4px', textTransform: 'uppercase', letterSpacing: '0.08em' }}>Status bar explained</p>
-            {getStatusItems(nodeCount, edgeCount).map(({ badge, title, desc }) => (
-                <div key={title} style={{ background: 'rgba(255,255,255,0.04)', borderRadius: 10, padding: '10px 14px', display: 'flex', gap: 12, alignItems: 'center' }}>
-                    {badge}
-                    <div>
-                        <p style={{ fontSize: 12, fontWeight: 500, color: '#e2e2e8', margin: '0 0 2px' }}>{title}</p>
-                        <p style={{ fontSize: 12, color: '#9ca3af', margin: 0 }}>{desc}</p>
-                    </div>
-                </div>
-            ))}
-        </div>
-    );
-
-    return null;
-}
-
-export const HelpPanel = ({ isOpen, onClose, nodeCount, edgeCount }: HelpPanelProps) => {
-    const [active, setActive] = useState<TabId>('overview');
-
-    if (!isOpen) return null;
-
-    return (
-        <div style={{ position: 'fixed', inset: 0, zIndex: 50, display: 'flex', alignItems: 'center', justifyContent: 'center' }}>
-            {/* Backdrop */}
-            <div
-                style={{ position: 'absolute', inset: 0, background: 'rgba(0,0,0,0.6)', backdropFilter: 'blur(4px)' }}
-                onClick={onClose}
-            />
-
-            {/* Panel */}
-            <div style={{
-                position: 'relative',
-                background: '#12121a',
-                border: '0.5px solid rgba(255,255,255,0.12)',
-                borderRadius: 16,
-                boxShadow: '0 25px 60px rgba(0,0,0,0.7)',
-                width: '100%',
-                maxWidth: 680,
-                margin: '0 16px',
-                height: '60vh',
-                display: 'flex',
-                flexDirection: 'column',
-                overflow: 'hidden',
-                fontFamily: 'var(--font-mono, monospace)',
-            }}>
-
-                {/* Header */}
-                <div style={{
-                    display: 'flex',
-                    alignItems: 'center',
-                    justifyContent: 'space-between',
-                    padding: '16px 20px',
-                    borderBottom: '0.5px solid rgba(255,255,255,0.08)',
-                    background: 'rgba(255,255,255,0.02)',
-                }}>
-                    <div style={{ display: 'flex', alignItems: 'center', gap: 12 }}>
-                        <div style={{ width: 40, height: 40, display: 'flex', alignItems: 'center', justifyContent: 'center', background: 'rgba(167,139,250,0.15)', borderRadius: 12 }}>
-                            <HelpCircle style={{ width: 20, height: 20, color: '#a78bfa' }} />
-                        </div>
-                        <div>
-                            <h2 style={{ fontSize: 16, fontWeight: 600, color: '#e2e2e8', margin: 0 }}>Help & Reference</h2>
-                            <p style={{ fontSize: 12, color: '#6b7280', margin: 0 }}>GitNexus — graph explorer</p>
-                        </div>
-                    </div>
-                    <button
-                        onClick={onClose}
-                        style={{ padding: 8, color: '#6b7280', background: 'transparent', border: 'none', borderRadius: 8, cursor: 'pointer', display: 'flex', alignItems: 'center', justifyContent: 'center', transition: 'color 0.15s' }}
-                        onMouseEnter={e => (e.currentTarget.style.color = '#e2e2e8')}
-                        onMouseLeave={e => (e.currentTarget.style.color = '#6b7280')}
-                    >
-                        <X style={{ width: 20, height: 20 }} />
-                    </button>
-                </div>
-
-                {/* Body: sidebar + content */}
-                <div style={{ display: 'grid', gridTemplateColumns: '168px 1fr', flex: 1, overflow: 'hidden' }}>
-
-                    {/* Sidebar nav */}
-                    <div style={{ borderRight: '0.5px solid rgba(255,255,255,0.08)', padding: '12px 8px', display: 'flex', flexDirection: 'column', gap: 2 }}>
-                        {tabs.map(({ id, label, icon }) => {
-                            const isActive = active === id;
-                            return (
-                                <button
-                                    key={id}
-                                    onClick={() => setActive(id)}
-                                    style={{
-                                        display: 'flex',
-                                        alignItems: 'center',
-                                        gap: 8,
-                                        textAlign: 'left',
-                                        background: isActive ? 'rgba(167,139,250,0.12)' : 'transparent',
-                                        border: 'none',
-                                        borderRadius: 8,
-                                        padding: '8px 10px',
-                                        fontSize: 12,
-                                        fontFamily: 'inherit',
-                                        color: isActive ? '#a78bfa' : '#9ca3af',
-                                        cursor: 'pointer',
-                                        transition: 'all 0.15s',
-                                        width: '100%',
-                                    }}
-                                    onMouseEnter={e => { if (!isActive) { e.currentTarget.style.color = '#e2e2e8'; e.currentTarget.style.background = 'rgba(255,255,255,0.04)'; } }}
-                                    onMouseLeave={e => { if (!isActive) { e.currentTarget.style.color = '#9ca3af'; e.currentTarget.style.background = 'transparent'; } }}
-                                >
-                                    <span style={{ color: isActive ? '#a78bfa' : '#6b7280', display: 'flex', flexShrink: 0 }}>{icon}</span>
-                                    {label}
-                                </button>
-                            );
-                        })}
-                    </div>
-
-                    {/* Content pane */}
-                    <div style={{ padding: '20px', overflowY: 'auto' }}>
-                        <TabContent active={active} nodeCount={nodeCount} edgeCount={edgeCount} />
-                    </div>
-                </div>
-
-                {/* Footer */}
-                <div style={{
-                    display: 'flex',
-                    alignItems: 'center',
-                    justifyContent: 'space-between',
-                    padding: '10px 20px',
-                    borderTop: '0.5px solid rgba(255,255,255,0.08)',
-                    background: 'rgba(255,255,255,0.01)',
-                }}>
-                    <span style={{ fontSize: 11, color: '#4b5563' }}>GitNexus — open source codebase graph explorer</span>
-                    <a
-                        href="https://github.com/abhigyanpatwari/GitNexus"
-                        target="_blank"
-                        rel="noopener noreferrer"
-                        style={{ fontSize: 11, color: '#a78bfa', textDecoration: 'none' }}
-                    >
-                        Docs & GitHub ↗
-                    </a>
-                </div>
-
-            </div>
-        </div>
-    );
-};

gitnexus-web/src/components/SettingsPanel.tsx

@@ -281,7 +281,7 @@ export const SettingsPanel = ({ isOpen, onClose, onSettingsSaved, backendUrl, is
 
   if (!isOpen) return null;
 
-  const providers: LLMProvider[] = ['openai', 'gemini', 'anthropic', 'azure-openai', 'ollama', 'openrouter', 'minimax'];
+  const providers: LLMProvider[] = ['openai', 'gemini', 'anthropic', 'azure-openai', 'ollama', 'openrouter'];
 
 
   return (
@@ -366,7 +366,7 @@ export const SettingsPanel = ({ isOpen, onClose, onSettingsSaved, backendUrl, is
                     w-8 h-8 rounded-lg flex items-center justify-center text-lg
                     ${settings.activeProvider === provider ? 'bg-accent/20' : 'bg-surface'}
                   `}>
-                    {provider === 'openai' ? '🤖' : provider === 'gemini' ? '💎' : provider === 'anthropic' ? '🧠' : provider === 'ollama' ? '🦙' : provider === 'openrouter' ? '🌐' : provider === 'minimax' ? '⚡' : '☁️'}
+                    {provider === 'openai' ? '🤖' : provider === 'gemini' ? '💎' : provider === 'anthropic' ? '🧠' : provider === 'ollama' ? '🦙' : provider === 'openrouter' ? '🌐' : '☁️'}
                   </div>
                   <span className="font-medium">{getProviderDisplayName(provider)}</span>
                 </button>
@@ -814,64 +814,7 @@ export const SettingsPanel = ({ isOpen, onClose, onSettingsSaved, backendUrl, is
             </div>
           )}
 
-          {/* MiniMax Settings */}
-          {settings.activeProvider === 'minimax' && (
-            <div className="space-y-4 animate-fade-in">
-              <div className="space-y-2">
-                <label className="flex items-center gap-2 text-sm font-medium text-text-secondary">
-                  <Key className="w-4 h-4" />
-                  API Key
-                </label>
-                <div className="relative">
-                  <input
-                    type={showApiKey['minimax'] ? 'text' : 'password'}
-                    value={settings.minimax?.apiKey ?? ''}
-                    onChange={e => setSettings(prev => ({
-                      ...prev,
-                      minimax: { ...prev.minimax!, apiKey: e.target.value }
-                    }))}
-                    placeholder="Enter your MiniMax API key"
-                    className="w-full px-4 py-3 pr-12 bg-elevated border border-border-subtle rounded-xl text-text-primary placeholder:text-text-muted focus:border-accent focus:ring-2 focus:ring-accent/20 outline-none transition-all"
-                  />
-                  <button
-                    type="button"
-                    onClick={() => toggleApiKeyVisibility('minimax')}
-                    className="absolute right-3 top-1/2 -translate-y-1/2 p-1 text-text-muted hover:text-text-primary transition-colors"
-                  >
-                    {showApiKey['minimax'] ? <EyeOff className="w-4 h-4" /> : <Eye className="w-4 h-4" />}
-                  </button>
-                </div>
-                <p className="text-xs text-text-muted">
-                  Get your API key from{' '}
-                  <a
-                    href="https://platform.minimax.io"
-                    target="_blank"
-                    rel="noopener noreferrer"
-                    className="text-accent hover:underline"
-                  >
-                    MiniMax Platform
-                  </a>
-                </p>
-              </div>
 
-              <div className="space-y-2">
-                <label className="text-sm font-medium text-text-secondary">Model</label>
-                <input
-                  type="text"
-                  value={settings.minimax?.model ?? 'MiniMax-M2.5'}
-                  onChange={e => setSettings(prev => ({
-                    ...prev,
-                    minimax: { ...prev.minimax!, model: e.target.value }
-                  }))}
-                  placeholder="e.g., MiniMax-M2.5, MiniMax-M2.5-highspeed"
-                  className="w-full px-4 py-3 bg-elevated border border-border-subtle rounded-xl text-text-primary placeholder:text-text-muted focus:border-accent focus:ring-2 focus:ring-accent/20 outline-none transition-all font-mono text-sm"
-                />
-                <p className="text-xs text-text-muted">
-                  Available models: MiniMax-M2.5 (default), MiniMax-M2.5-highspeed (faster)
-                </p>
-              </div>
-            </div>
-          )}
 
           {/* Privacy Note */}
           <div className="p-4 bg-elevated/50 border border-border-subtle rounded-xl">

gitnexus-web/src/config/supported-languages.ts

@@ -9,7 +9,6 @@ export enum SupportedLanguages {
     Go = 'go',
     Rust = 'rust',
     PHP = 'php',
-    Ruby = 'ruby',
-    Kotlin = 'kotlin',
+    // Ruby = 'ruby',
     Swift = 'swift',
 }

gitnexus-web/src/core/embeddings/embedder.ts

@@ -275,7 +275,7 @@ export const embedBatch = async (texts: string[]): Promise<Float32Array[]> => {
 };
 
 /**
- * Convert Float32Array to regular number array (for LadybugDB storage)
+ * Convert Float32Array to regular number array (for KuzuDB storage)
  */
 export const embeddingToArray = (embedding: Float32Array): number[] => {
   return Array.from(embedding);

gitnexus-web/src/core/embeddings/embedding-pipeline.ts

@@ -2,10 +2,10 @@
  * Embedding Pipeline Module
  * 
  * Orchestrates the background embedding process:
- * 1. Query embeddable nodes from LadybugDB
+ * 1. Query embeddable nodes from KuzuDB
  * 2. Generate text representations
  * 3. Batch embed using transformers.js
- * 4. Update LadybugDB with embeddings
+ * 4. Update KuzuDB with embeddings
  * 5. Create vector index for semantic search
  */
 
@@ -27,7 +27,7 @@ import {
 export type EmbeddingProgressCallback = (progress: EmbeddingProgress) => void;
 
 /**
- * Query all embeddable nodes from LadybugDB
+ * Query all embeddable nodes from KuzuDB
  * Uses table-specific queries (File has different schema than code elements)
  */
 const queryEmbeddableNodes = async (
@@ -102,23 +102,9 @@ const batchInsertEmbeddings = async (
  * Create the vector index for semantic search
  * Now indexes the separate CodeEmbedding table
  */
-let vectorExtensionLoaded = false;
-
 const createVectorIndex = async (
   executeQuery: (cypher: string) => Promise<any[]>
 ): Promise<void> => {
-  // LadybugDB v0.15+ requires explicit VECTOR extension loading (once per session)
-  if (!vectorExtensionLoaded) {
-    try {
-      await executeQuery('INSTALL VECTOR');
-      await executeQuery('LOAD EXTENSION VECTOR');
-      vectorExtensionLoaded = true;
-    } catch {
-      // Extension may already be loaded — CREATE_VECTOR_INDEX will fail clearly if not
-      vectorExtensionLoaded = true;
-    }
-  }
-
   const cypher = `
     CALL CREATE_VECTOR_INDEX('CodeEmbedding', 'code_embedding_idx', 'embedding', metric := 'cosine')
   `;
@@ -136,7 +122,7 @@ const createVectorIndex = async (
 /**
  * Run the embedding pipeline
  * 
- * @param executeQuery - Function to execute Cypher queries against LadybugDB
+ * @param executeQuery - Function to execute Cypher queries against KuzuDB
  * @param executeWithReusedStatement - Function to execute with reused prepared statement
  * @param onProgress - Callback for progress updates
  * @param config - Optional configuration override
@@ -220,7 +206,7 @@ export const runEmbeddingPipeline = async (
       // Embed the batch
       const embeddings = await embedBatch(texts);
 
-      // Update LadybugDB with embeddings
+      // Update KuzuDB with embeddings
       const updates = batch.map((node, i) => ({
         id: node.id,
         embedding: embeddingToArray(embeddings[i]),
@@ -327,64 +313,51 @@ export const semanticSearch = async (
     return [];
   }
 
-  // Group results by label for batched metadata queries
-  const byLabel = new Map<string, Array<{ nodeId: string; distance: number }>>();
+  // Get metadata for each result by querying each node table
+  const results: SemanticSearchResult[] = [];
+  
   for (const embRow of embResults) {
     const nodeId = embRow.nodeId ?? embRow[0];
     const distance = embRow.distance ?? embRow[1];
+    
+    // Extract label from node ID (format: Label:path:name)
     const labelEndIdx = nodeId.indexOf(':');
     const label = labelEndIdx > 0 ? nodeId.substring(0, labelEndIdx) : 'Unknown';
-    if (!byLabel.has(label)) byLabel.set(label, []);
-    byLabel.get(label)!.push({ nodeId, distance });
-  }
-
-  // Batch-fetch metadata per label
-  const results: SemanticSearchResult[] = [];
-
-  for (const [label, items] of byLabel) {
-    const idList = items.map(i => `'${i.nodeId.replace(/'/g, "''")}'`).join(', ');
+    
+    // Query the specific table for this node
+    // File nodes don't have startLine/endLine
     try {
       let nodeQuery: string;
       if (label === 'File') {
         nodeQuery = `
-          MATCH (n:File) WHERE n.id IN [${idList}]
-          RETURN n.id AS id, n.name AS name, n.filePath AS filePath
+          MATCH (n:File {id: '${nodeId.replace(/'/g, "''")}'}) 
+          RETURN n.name AS name, n.filePath AS filePath
         `;
       } else {
         nodeQuery = `
-          MATCH (n:${label}) WHERE n.id IN [${idList}]
-          RETURN n.id AS id, n.name AS name, n.filePath AS filePath,
+          MATCH (n:${label} {id: '${nodeId.replace(/'/g, "''")}'}) 
+          RETURN n.name AS name, n.filePath AS filePath, 
                  n.startLine AS startLine, n.endLine AS endLine
         `;
       }
       const nodeRows = await executeQuery(nodeQuery);
-      const rowMap = new Map<string, any>();
-      for (const row of nodeRows) {
-        const id = row.id ?? row[0];
-        rowMap.set(id, row);
-      }
-      for (const item of items) {
-        const nodeRow = rowMap.get(item.nodeId);
-        if (nodeRow) {
-          results.push({
-            nodeId: item.nodeId,
-            name: nodeRow.name ?? nodeRow[1] ?? '',
-            label,
-            filePath: nodeRow.filePath ?? nodeRow[2] ?? '',
-            distance: item.distance,
-            startLine: label !== 'File' ? (nodeRow.startLine ?? nodeRow[3]) : undefined,
-            endLine: label !== 'File' ? (nodeRow.endLine ?? nodeRow[4]) : undefined,
-          });
-        }
+      if (nodeRows.length > 0) {
+        const nodeRow = nodeRows[0];
+        results.push({
+          nodeId,
+          name: nodeRow.name ?? nodeRow[0] ?? '',
+          label,
+          filePath: nodeRow.filePath ?? nodeRow[1] ?? '',
+          distance,
+          startLine: label !== 'File' ? (nodeRow.startLine ?? nodeRow[2]) : undefined,
+          endLine: label !== 'File' ? (nodeRow.endLine ?? nodeRow[3]) : undefined,
+        });
       }
     } catch {
       // Table might not exist, skip
     }
   }
 
-  // Re-sort by distance since batch queries may have mixed order
-  results.sort((a, b) => a.distance - b.distance);
-
   return results;
 };
 

gitnexus-web/src/core/embeddings/types.ts

@@ -92,7 +92,7 @@ export interface SemanticSearchResult {
 }
 
 /**
- * Node data for embedding (minimal structure from LadybugDB query)
+ * Node data for embedding (minimal structure from KuzuDB query)
  */
 export interface EmbeddableNode {
   id: string;

gitnexus-web/src/core/graph/types.ts

@@ -54,7 +54,6 @@ export type RelationshipType =
   | 'DECORATES'
   | 'IMPLEMENTS'
   | 'EXTENDS'
-  | 'HAS_METHOD'
   | 'MEMBER_OF'
   | 'STEP_IN_PROCESS'
 

gitnexus-web/src/core/ingestion/call-processor.ts

@@ -6,7 +6,6 @@ import { loadParser, loadLanguage } from '../tree-sitter/parser-loader';
 import { LANGUAGE_QUERIES } from './tree-sitter-queries';
 import { generateId } from '../../lib/utils';
 import { getLanguageFromFilename } from './utils';
-import { callRouters } from './call-routing';
 
 /**
  * Node types that represent function/method definitions across languages.
@@ -36,9 +35,6 @@ const FUNCTION_NODE_TYPES = new Set([
   // Rust
   'function_item',
   'impl_item', // Methods inside impl blocks
-  // Ruby
-  'method',           // def foo
-  'singleton_method', // def self.foo
 ]);
 
 /**
@@ -96,18 +92,6 @@ const findEnclosingFunction = (
                          current.children?.find((c: any) => c.type === 'identifier');
         funcName = nameNode?.text;
         label = 'Method'; // Treat constructors as methods for process detection
-      } else if (current.type === 'method') {
-        // Ruby instance method: def foo
-        const nameNode = current.childForFieldName?.('name') ||
-                         current.children?.find((c: any) => c.type === 'identifier');
-        funcName = nameNode?.text;
-        label = 'Method';
-      } else if (current.type === 'singleton_method') {
-        // Ruby class method: def self.foo
-        const nameNode = current.childForFieldName?.('name') ||
-                         current.children?.find((c: any) => c.type === 'identifier');
-        funcName = nameNode?.text;
-        label = 'Method';
       } else if (current.type === 'arrow_function' || current.type === 'function_expression') {
         // Arrow/expression: const foo = () => {} - check parent variable declarator
         const parent = current.parent;
@@ -142,47 +126,6 @@ const findEnclosingFunction = (
   return null; // Top-level call (not inside any function)
 };
 
-/** AST node types that represent a class-like container */
-const CLASS_CONTAINER_TYPES = new Set([
-  'class_declaration', 'abstract_class_declaration',
-  'interface_declaration', 'struct_declaration', 'record_declaration',
-  'class_specifier', 'struct_specifier',
-  'impl_item', 'trait_item',
-  'class_definition',
-  'trait_declaration',
-  'protocol_declaration',
-  'class', 'module', // Ruby
-]);
-
-const CONTAINER_TYPE_TO_LABEL: Record<string, string> = {
-  class_declaration: 'Class', abstract_class_declaration: 'Class',
-  interface_declaration: 'Interface',
-  struct_declaration: 'Struct', struct_specifier: 'Struct',
-  class_specifier: 'Class', class_definition: 'Class',
-  impl_item: 'Impl', trait_item: 'Trait', trait_declaration: 'Trait',
-  record_declaration: 'Record', protocol_declaration: 'Interface',
-  class: 'Class', module: 'Module',
-};
-
-/** Walk up AST to find enclosing class/struct/interface, return its generateId or null. */
-const findEnclosingClassId = (node: any, filePath: string): string | null => {
-  let current = node.parent;
-  while (current) {
-    if (CLASS_CONTAINER_TYPES.has(current.type)) {
-      const nameNode = current.childForFieldName?.('name')
-        ?? current.children?.find((c: any) =>
-          c.type === 'type_identifier' || c.type === 'identifier' || c.type === 'name' || c.type === 'constant'
-        );
-      if (nameNode) {
-        const label = CONTAINER_TYPE_TO_LABEL[current.type] || 'Class';
-        return generateId(label, `${filePath}:${nameNode.text}`);
-      }
-    }
-    current = current.parent;
-  }
-  return null;
-};
-
 export const processCalls = async (
   graph: KnowledgeGraph,
   files: { path: string; content: string }[],
@@ -228,8 +171,6 @@ export const processCalls = async (
       continue;
     }
 
-    const callRouter = callRouters[language];
-
     // 3. Process each call match
     matches.forEach(match => {
       const captureMap: Record<string, any> = {};
@@ -243,68 +184,6 @@ export const processCalls = async (
 
       const calledName = nameNode.text;
 
-      // Dispatch: route language-specific calls (heritage, properties, imports)
-      const routed = callRouter(calledName, captureMap['call']);
-      if (routed) {
-        switch (routed.kind) {
-          case 'skip':
-          case 'import': // handled by import-processor
-            return;
-
-          case 'heritage':
-            for (const item of routed.items) {
-              const childId = symbolTable.lookupExact(file.path, item.enclosingClass) ||
-                              symbolTable.lookupFuzzy(item.enclosingClass)[0]?.nodeId ||
-                              generateId('Class', `${file.path}:${item.enclosingClass}`);
-              const parentId = symbolTable.lookupFuzzy(item.mixinName)[0]?.nodeId ||
-                               generateId('Module', `${item.mixinName}`);
-              if (childId && parentId) {
-                const relId = generateId('IMPLEMENTS', `${childId}->${parentId}:${item.heritageKind}`);
-                graph.addRelationship({
-                  id: relId, sourceId: childId, targetId: parentId,
-                  type: 'IMPLEMENTS', confidence: 1.0, reason: item.heritageKind,
-                });
-              }
-            }
-            return;
-
-          case 'properties': {
-            const fileId = generateId('File', file.path);
-            const propEnclosingClassId = findEnclosingClassId(captureMap['call'], file.path);
-            for (const item of routed.items) {
-              const nodeId = generateId('Property', `${file.path}:${item.propName}`);
-              graph.addNode({
-                id: nodeId,
-                label: 'Property' as any, // TODO: add 'Property' to graph node label union
-                properties: {
-                  name: item.propName, filePath: file.path,
-                  startLine: item.startLine, endLine: item.endLine,
-                  language, isExported: true,
-                  description: item.accessorType,
-                },
-              });
-              symbolTable.add(file.path, item.propName, nodeId, 'Property');
-              const relId = generateId('DEFINES', `${fileId}->${nodeId}`);
-              graph.addRelationship({
-                id: relId, sourceId: fileId, targetId: nodeId,
-                type: 'DEFINES', confidence: 1.0, reason: '',
-              });
-              if (propEnclosingClassId) {
-                graph.addRelationship({
-                  id: generateId('HAS_METHOD', `${propEnclosingClassId}->${nodeId}`),
-                  sourceId: propEnclosingClassId, targetId: nodeId,
-                  type: 'HAS_METHOD', confidence: 1.0, reason: '',
-                });
-              }
-            }
-            return;
-          }
-
-          case 'call':
-            break; // fall through to normal call processing below
-        }
-      }
-
       // Skip common built-ins and noise
       if (isBuiltInOrNoise(calledName)) return;
 
@@ -321,10 +200,10 @@ export const processCalls = async (
       // 5. Find the enclosing function (caller)
       const callNode = captureMap['call'];
       const enclosingFuncId = findEnclosingFunction(callNode, file.path, symbolTable);
-
+      
       // Use enclosing function as source, fallback to file for top-level calls
       const sourceId = enclosingFuncId || generateId('File', file.path);
-
+      
       const relId = generateId('CALLS', `${sourceId}:${calledName}->${resolved.nodeId}`);
 
       graph.addRelationship({
@@ -832,72 +711,37 @@ const resolveCallTarget = (
  * Filter out common built-in functions and noise
  * that shouldn't be tracked as calls
  */
-/** Pre-built set (module-level singleton) to avoid re-creating per call */
-const BUILT_IN_NAMES = new Set([
-  // JavaScript/TypeScript built-ins
-  'console', 'log', 'warn', 'error', 'info', 'debug',
-  'setTimeout', 'setInterval', 'clearTimeout', 'clearInterval',
-  'parseInt', 'parseFloat', 'isNaN', 'isFinite',
-  'encodeURI', 'decodeURI', 'encodeURIComponent', 'decodeURIComponent',
-  'JSON', 'parse', 'stringify',
-  'Object', 'Array', 'String', 'Number', 'Boolean', 'Symbol', 'BigInt',
-  'Map', 'Set', 'WeakMap', 'WeakSet',
-  'Promise', 'resolve', 'reject', 'then', 'catch', 'finally',
-  'Math', 'Date', 'RegExp', 'Error',
-  'require', 'import', 'export',
-  'fetch', 'Response', 'Request',
-  // React hooks and common functions
-  'useState', 'useEffect', 'useCallback', 'useMemo', 'useRef', 'useContext',
-  'useReducer', 'useLayoutEffect', 'useImperativeHandle', 'useDebugValue',
-  'createElement', 'createContext', 'createRef', 'forwardRef', 'memo', 'lazy',
-  // Common array/object methods
-  'map', 'filter', 'reduce', 'forEach', 'find', 'findIndex', 'some', 'every',
-  'includes', 'indexOf', 'slice', 'splice', 'concat', 'join', 'split',
-  'push', 'pop', 'shift', 'unshift', 'sort', 'reverse',
-  'keys', 'values', 'entries', 'assign', 'freeze', 'seal',
-  'hasOwnProperty', 'toString', 'valueOf',
-  // Python built-ins
-  'print', 'len', 'range', 'str', 'int', 'float', 'list', 'dict', 'set', 'tuple',
-  'open', 'read', 'write', 'close', 'append', 'extend', 'update',
-  'super', 'type', 'isinstance', 'issubclass', 'getattr', 'setattr', 'hasattr',
-  'enumerate', 'zip', 'sorted', 'reversed', 'min', 'max', 'sum', 'abs',
-  // C/C++ standard library and common kernel helpers
-  'printf', 'fprintf', 'sprintf', 'snprintf', 'vprintf', 'vfprintf', 'vsprintf', 'vsnprintf',
-  'scanf', 'fscanf', 'sscanf',
-  'malloc', 'calloc', 'realloc', 'free', 'memcpy', 'memmove', 'memset', 'memcmp',
-  'strlen', 'strcpy', 'strncpy', 'strcat', 'strncat', 'strcmp', 'strncmp', 'strstr', 'strchr', 'strrchr',
-  'atoi', 'atol', 'atof', 'strtol', 'strtoul', 'strtoll', 'strtoull', 'strtod',
-  'sizeof', 'offsetof', 'typeof',
-  'assert', 'abort', 'exit', '_exit',
-  'fopen', 'fclose', 'fread', 'fwrite', 'fseek', 'ftell', 'rewind', 'fflush', 'fgets', 'fputs',
-  // Linux kernel common macros/helpers (not real call targets)
-  'likely', 'unlikely', 'BUG', 'BUG_ON', 'WARN', 'WARN_ON', 'WARN_ONCE',
-  'IS_ERR', 'PTR_ERR', 'ERR_PTR', 'IS_ERR_OR_NULL',
-  'ARRAY_SIZE', 'container_of', 'list_for_each_entry', 'list_for_each_entry_safe',
-  'min', 'max', 'clamp', 'abs', 'swap',
-  'pr_info', 'pr_warn', 'pr_err', 'pr_debug', 'pr_notice', 'pr_crit', 'pr_emerg',
-  'printk', 'dev_info', 'dev_warn', 'dev_err', 'dev_dbg',
-  'GFP_KERNEL', 'GFP_ATOMIC',
-  'spin_lock', 'spin_unlock', 'spin_lock_irqsave', 'spin_unlock_irqrestore',
-  'mutex_lock', 'mutex_unlock', 'mutex_init',
-  'kfree', 'kmalloc', 'kzalloc', 'kcalloc', 'krealloc', 'kvmalloc', 'kvfree',
-  'get', 'put',
-  // Ruby built-ins and Kernel methods
-  'puts', 'print', 'p', 'pp', 'warn', 'raise', 'fail',
-  'require', 'require_relative', 'load', 'autoload',
-  'include', 'extend', 'prepend',
-  'attr_accessor', 'attr_reader', 'attr_writer',
-  'public', 'private', 'protected', 'module_function',
-  'lambda', 'proc', 'block_given?',
-  'nil?', 'is_a?', 'kind_of?', 'instance_of?', 'respond_to?',
-  'freeze', 'frozen?', 'dup', 'clone', 'tap', 'then', 'yield_self',
-  // Ruby enumerables
-  'each', 'map', 'select', 'reject', 'find', 'detect', 'collect',
-  'inject', 'reduce', 'flat_map', 'each_with_object', 'each_with_index',
-  'any?', 'all?', 'none?', 'count', 'first', 'last',
-  'sort', 'sort_by', 'min', 'max', 'min_by', 'max_by',
-  'group_by', 'partition', 'zip', 'compact', 'flatten', 'uniq',
-]);
+const isBuiltInOrNoise = (name: string): boolean => {
+  const builtIns = new Set([
+    // JavaScript/TypeScript built-ins
+    'console', 'log', 'warn', 'error', 'info', 'debug',
+    'setTimeout', 'setInterval', 'clearTimeout', 'clearInterval',
+    'parseInt', 'parseFloat', 'isNaN', 'isFinite',
+    'encodeURI', 'decodeURI', 'encodeURIComponent', 'decodeURIComponent',
+    'JSON', 'parse', 'stringify',
+    'Object', 'Array', 'String', 'Number', 'Boolean', 'Symbol', 'BigInt',
+    'Map', 'Set', 'WeakMap', 'WeakSet',
+    'Promise', 'resolve', 'reject', 'then', 'catch', 'finally',
+    'Math', 'Date', 'RegExp', 'Error',
+    'require', 'import', 'export',
+    'fetch', 'Response', 'Request',
+    // React hooks and common functions
+    'useState', 'useEffect', 'useCallback', 'useMemo', 'useRef', 'useContext',
+    'useReducer', 'useLayoutEffect', 'useImperativeHandle', 'useDebugValue',
+    'createElement', 'createContext', 'createRef', 'forwardRef', 'memo', 'lazy',
+    // Common array/object methods
+    'map', 'filter', 'reduce', 'forEach', 'find', 'findIndex', 'some', 'every',
+    'includes', 'indexOf', 'slice', 'splice', 'concat', 'join', 'split',
+    'push', 'pop', 'shift', 'unshift', 'sort', 'reverse',
+    'keys', 'values', 'entries', 'assign', 'freeze', 'seal',
+    'hasOwnProperty', 'toString', 'valueOf',
+    // Python built-ins
+    'print', 'len', 'range', 'str', 'int', 'float', 'list', 'dict', 'set', 'tuple',
+    'open', 'read', 'write', 'close', 'append', 'extend', 'update',
+    'super', 'type', 'isinstance', 'issubclass', 'getattr', 'setattr', 'hasattr',
+    'enumerate', 'zip', 'sorted', 'reversed', 'min', 'max', 'sum', 'abs',
+  ]);
 
-const isBuiltInOrNoise = (name: string): boolean => BUILT_IN_NAMES.has(name);
+  return builtIns.has(name);
+};
 

gitnexus-web/src/core/ingestion/call-routing.ts

@@ -1,149 +0,0 @@
-/**
- * Shared Ruby call routing logic.
- *
- * Ruby expresses imports, heritage (mixins), and property definitions as
- * method calls rather than syntax-level constructs. This module provides a
- * routing function used by the CLI call-processor, CLI parse-worker, and
- * the web call-processor so that the classification logic lives in one place.
- *
- * NOTE: This file is intentionally duplicated in gitnexus-web/ because the
- * two packages have separate build targets (Node native vs WASM/browser).
- * Keep both copies in sync until a shared package is introduced.
- */
-
-import { SupportedLanguages } from '../../config/supported-languages';
-
-// ── Call routing dispatch table ─────────────────────────────────────────────
-
-/** null = this call was not routed; fall through to default call handling */
-export type CallRoutingResult = RubyCallRouting | null;
-
-export type CallRouter = (
-  calledName: string,
-  callNode: any,
-) => CallRoutingResult;
-
-/** No-op router: returns null for every call (passthrough to normal processing) */
-const noRouting: CallRouter = () => null;
-
-/** Per-language call routing. noRouting = no special routing (normal call processing) */
-export const callRouters = {
-  [SupportedLanguages.JavaScript]: noRouting,
-  [SupportedLanguages.TypeScript]: noRouting,
-  [SupportedLanguages.Python]: noRouting,
-  [SupportedLanguages.Java]: noRouting,
-  [SupportedLanguages.Go]: noRouting,
-  [SupportedLanguages.Rust]: noRouting,
-  [SupportedLanguages.CSharp]: noRouting,
-  [SupportedLanguages.PHP]: noRouting,
-  [SupportedLanguages.Swift]: noRouting,
-  [SupportedLanguages.CPlusPlus]: noRouting,
-  [SupportedLanguages.C]: noRouting,
-  [SupportedLanguages.Ruby]: routeRubyCall,
-  [SupportedLanguages.Kotlin]: noRouting,
-} satisfies Record<SupportedLanguages, CallRouter>;
-
-// ── Result types ────────────────────────────────────────────────────────────
-
-export type RubyCallRouting =
-  | { kind: 'import'; importPath: string; isRelative: boolean }
-  | { kind: 'heritage'; items: RubyHeritageItem[] }
-  | { kind: 'properties'; items: RubyPropertyItem[] }
-  | { kind: 'call' }
-  | { kind: 'skip' };
-
-export interface RubyHeritageItem {
-  enclosingClass: string;
-  mixinName: string;
-  heritageKind: 'include' | 'extend' | 'prepend';
-}
-
-export type RubyAccessorType = 'attr_accessor' | 'attr_reader' | 'attr_writer';
-
-export interface RubyPropertyItem {
-  propName: string;
-  accessorType: RubyAccessorType;
-  startLine: number;
-  endLine: number;
-}
-
-// ── Pre-allocated singletons for common return values ────────────────────────
-const CALL_RESULT: RubyCallRouting = { kind: 'call' };
-const SKIP_RESULT: RubyCallRouting = { kind: 'skip' };
-
-/** Max depth for parent-walking loops to prevent pathological AST traversals */
-const MAX_PARENT_DEPTH = 50;
-
-// ── Routing function ────────────────────────────────────────────────────────
-
-/**
- * Classify a Ruby call node and extract its semantic payload.
- *
- * @param calledName - The method name (e.g. 'require', 'include', 'attr_accessor')
- * @param callNode   - The tree-sitter `call` AST node
- * @returns A discriminated union describing the call's semantic role
- */
-export function routeRubyCall(calledName: string, callNode: any): RubyCallRouting {
-  // ── require / require_relative → import ─────────────────────────────────
-  if (calledName === 'require' || calledName === 'require_relative') {
-    const argList = callNode.childForFieldName?.('arguments');
-    const stringNode = argList?.children?.find((c: any) => c.type === 'string');
-    const contentNode = stringNode?.children?.find((c: any) => c.type === 'string_content');
-    if (!contentNode) return SKIP_RESULT;
-
-    let importPath: string = contentNode.text;
-    // Validate: reject null bytes, control chars, excessively long paths
-    if (!importPath || importPath.length > 1024 || /[\x00-\x1f]/.test(importPath)) {
-      return SKIP_RESULT;
-    }
-    const isRelative = calledName === 'require_relative';
-    if (isRelative && !importPath.startsWith('.')) {
-      importPath = './' + importPath;
-    }
-    return { kind: 'import', importPath, isRelative };
-  }
-
-  // ── include / extend / prepend → heritage (mixin) ──────────────────────
-  if (calledName === 'include' || calledName === 'extend' || calledName === 'prepend') {
-    let enclosingClass: string | null = null;
-    let current = callNode.parent;
-    let depth = 0;
-    while (current && ++depth <= MAX_PARENT_DEPTH) {
-      if (current.type === 'class' || current.type === 'module') {
-        const nameNode = current.childForFieldName?.('name');
-        if (nameNode) { enclosingClass = nameNode.text; break; }
-      }
-      current = current.parent;
-    }
-    if (!enclosingClass) return SKIP_RESULT;
-
-    const items: RubyHeritageItem[] = [];
-    const argList = callNode.childForFieldName?.('arguments');
-    for (const arg of (argList?.children ?? [])) {
-      if (arg.type === 'constant' || arg.type === 'scope_resolution') {
-        items.push({ enclosingClass, mixinName: arg.text, heritageKind: calledName as 'include' | 'extend' | 'prepend' });
-      }
-    }
-    return items.length > 0 ? { kind: 'heritage', items } : SKIP_RESULT;
-  }
-
-  // ── attr_accessor / attr_reader / attr_writer → property definitions ───
-  if (calledName === 'attr_accessor' || calledName === 'attr_reader' || calledName === 'attr_writer') {
-    const items: RubyPropertyItem[] = [];
-    const argList = callNode.childForFieldName?.('arguments');
-    for (const arg of (argList?.children ?? [])) {
-      if (arg.type === 'simple_symbol') {
-        items.push({
-          propName: arg.text.startsWith(':') ? arg.text.slice(1) : arg.text,
-          accessorType: calledName as RubyAccessorType,
-          startLine: arg.startPosition.row,
-          endLine: arg.endPosition.row,
-        });
-      }
-    }
-    return items.length > 0 ? { kind: 'properties', items } : SKIP_RESULT;
-  }
-
-  // ── Everything else → regular call ─────────────────────────────────────
-  return CALL_RESULT;
-}

gitnexus-web/src/core/ingestion/community-processor.ts

@@ -330,20 +330,25 @@ const calculateCohesion = (memberIds: string[], graph: Graph): number => {
 
   const memberSet = new Set(memberIds);
   let internalEdges = 0;
-  let totalEdges = 0;
-
-  // Count internal vs total edges for community members
+  
+  // Count edges within the community
   memberIds.forEach(nodeId => {
     if (graph.hasNode(nodeId)) {
       graph.forEachNeighbor(nodeId, neighbor => {
-        totalEdges++;
         if (memberSet.has(neighbor)) {
           internalEdges++;
         }
       });
     }
   });
-
-  if (totalEdges === 0) return 1.0;
-  return Math.min(1.0, internalEdges / totalEdges);
+  
+  // Each edge is counted twice (once from each end), so divide by 2
+  internalEdges = internalEdges / 2;
+  
+  // Maximum possible internal edges for n nodes: n*(n-1)/2
+  const maxPossibleEdges = (memberIds.length * (memberIds.length - 1)) / 2;
+  
+  if (maxPossibleEdges === 0) return 1.0;
+  
+  return Math.min(1.0, internalEdges / maxPossibleEdges);
 };

gitnexus-web/src/core/ingestion/entry-point-scoring.ts

@@ -13,7 +13,7 @@
 import { detectFrameworkFromPath } from './framework-detection';
 
 // ============================================================================
-// NAME PATTERNS - All 11 supported languages
+// NAME PATTERNS - All 9 supported languages
 // ============================================================================
 
 /**
@@ -143,13 +143,6 @@ const ENTRY_POINT_PATTERNS: Record<string, RegExp[]> = {
     /^save$/,                 // Repository::save()
     /^delete$/,               // Repository::delete()
   ],
-
-  // Ruby
-  'ruby': [
-    /^call$/,                 // Service objects (MyService.call)
-    /^perform$/,              // Background jobs (Sidekiq, ActiveJob)
-    /^execute$/,              // Command pattern
-  ],
 };
 
 // ============================================================================
@@ -309,12 +302,7 @@ export function isTestFile(filePath: string): boolean {
     p.endsWith('test.php') ||
     p.endsWith('spec.php') ||
     p.includes('/tests/feature/') ||
-    p.includes('/tests/unit/') ||
-    // Ruby test patterns
-    p.endsWith('_spec.rb') ||
-    p.endsWith('_test.rb') ||
-    p.includes('/spec/') ||
-    p.includes('/test/fixtures/')
+    p.includes('/tests/unit/')
   );
 }
 

gitnexus-web/src/core/ingestion/framework-detection.ts

@@ -257,17 +257,6 @@ export function detectFrameworkFromPath(filePath: string): FrameworkHint | null
     return { framework: 'laravel', entryPointMultiplier: 1.5, reason: 'laravel-repository' };
   }
 
-  // ========== RUBY ==========
-
-  // Ruby: bin/ or exe/ (CLI entry points)
-  if ((p.includes('/bin/') || p.includes('/exe/')) && p.endsWith('.rb')) {
-    return { framework: 'ruby', entryPointMultiplier: 2.5, reason: 'ruby-executable' };
-  }
-
-  // Ruby: Rakefile or *.rake (task definitions)
-  if (p.endsWith('/rakefile') || p.endsWith('.rake')) {
-    return { framework: 'ruby', entryPointMultiplier: 1.5, reason: 'ruby-rake' };
-  }
   // ========== SWIFT / iOS ==========
 
   // iOS App entry points (highest priority)

gitnexus-web/src/core/ingestion/import-processor.ts

@@ -4,7 +4,6 @@ import { loadParser, loadLanguage } from '../tree-sitter/parser-loader';
 import { LANGUAGE_QUERIES } from './tree-sitter-queries';
 import { generateId } from '../../lib/utils';
 import { getLanguageFromFilename } from './utils';
-import { callRouters } from './call-routing';
 
 // Type: Map<FilePath, Set<ResolvedFilePath>>
 // Stores all files that a given file imports from
@@ -54,9 +53,7 @@ const resolveImportPath = (
     // Go
     '.go',
     // Rust
-    '.rs', '/mod.rs',
-    // Ruby
-    '.rb', '.rake',
+    '.rs', '/mod.rs'
   ];
   
   if (importPath.startsWith('.')) {
@@ -223,35 +220,6 @@ export const processImports = async (
           importMap.get(file.path)!.add(resolvedPath);
         }
       }
-
-      // ---- Language-specific call-as-import routing (Ruby require, etc.) ----
-      if (captureMap['call']) {
-        const callNameNode = captureMap['call.name'];
-        if (callNameNode) {
-          const callRouter = callRouters[language];
-          const routed = callRouter(callNameNode.text, captureMap['call']);
-          if (routed && routed.kind === 'import') {
-            totalImportsFound++;
-            const resolvedPath = resolveImportPath(
-              file.path, routed.importPath, allFilePaths, allFileList, resolveCache
-            );
-            if (resolvedPath) {
-              const sourceId = generateId('File', file.path);
-              const targetId = generateId('File', resolvedPath);
-              const relId = generateId('IMPORTS', `${file.path}->${resolvedPath}`);
-              totalImportsResolved++;
-              graph.addRelationship({
-                id: relId, sourceId, targetId,
-                type: 'IMPORTS', confidence: 1.0, reason: '',
-              });
-              if (!importMap.has(file.path)) {
-                importMap.set(file.path, new Set());
-              }
-              importMap.get(file.path)!.add(resolvedPath);
-            }
-          }
-        }
-      }
     });
 
     // If re-parsed just for this, delete the tree to save memory

gitnexus-web/src/core/ingestion/parsing-processor.ts

@@ -14,7 +14,7 @@ export type FileProgressCallback = (current: number, total: number, filePath: st
 
 /**
  * Check if a symbol (function, class, etc.) is exported/public
- * Handles all 11 supported languages with explicit logic
+ * Handles all 9 supported languages with explicit logic
  * 
  * @param node - The AST node for the symbol name
  * @param name - The symbol name
@@ -104,11 +104,7 @@ const isNodeExported = (node: any, name: string, language: string): boolean => {
     case 'c':
     case 'cpp':
       return false;
-
-    // Ruby: All top-level definitions are public by default
-    case 'ruby':
-      return true;
-
+    
     default:
       return false;
   }

gitnexus-web/src/core/ingestion/tree-sitter-queries.ts

@@ -396,40 +396,6 @@ export const PHP_QUERIES = `
       [(name) (qualified_name)] @heritage.trait))) @heritage
 `;
 
-// Ruby queries - works with tree-sitter-ruby
-// NOTE: Ruby uses `call` for require, include, extend, prepend, attr_* etc.
-// These are all captured as @call and routed in JS post-processing:
-//   - require/require_relative → import extraction
-//   - include/extend/prepend → heritage (mixin) extraction
-//   - attr_accessor/attr_reader/attr_writer → property definition extraction
-//   - everything else → regular call extraction
-export const RUBY_QUERIES = `
-; ── Modules ──────────────────────────────────────────────────────────────────
-(module
-  name: (constant) @name) @definition.module
-
-; ── Classes ──────────────────────────────────────────────────────────────────
-(class
-  name: (constant) @name) @definition.class
-
-; ── Instance methods ─────────────────────────────────────────────────────────
-(method
-  name: (identifier) @name) @definition.method
-
-; ── Singleton (class-level) methods ──────────────────────────────────────────
-(singleton_method
-  name: (identifier) @name) @definition.function
-
-; ── All calls (require, include, attr_*, and regular calls routed in JS) ─────
-(call
-  method: (identifier) @call.name) @call
-
-; ── Heritage: class < SuperClass ─────────────────────────────────────────────
-(class
-  name: (constant) @heritage.class
-  superclass: (superclass
-    (constant) @heritage.extends)) @heritage`;
-    
 // Swift queries - works with tree-sitter-swift
 export const SWIFT_QUERIES = `
 ; Classes
@@ -494,8 +460,6 @@ export const LANGUAGE_QUERIES: Record<SupportedLanguages, string> = {
   [SupportedLanguages.CSharp]: CSHARP_QUERIES,
   [SupportedLanguages.Rust]: RUST_QUERIES,
   [SupportedLanguages.PHP]: PHP_QUERIES,
-  [SupportedLanguages.Ruby]: RUBY_QUERIES,
-  [SupportedLanguages.Kotlin]: '', // Kotlin WASM parser not yet available for web
   [SupportedLanguages.Swift]: SWIFT_QUERIES,
 };
  

gitnexus-web/src/core/ingestion/utils.ts

@@ -1,8 +1,5 @@
 import { SupportedLanguages } from '../../config/supported-languages';
 
-/** Ruby extensionless filenames recognised as Ruby source */
-const RUBY_EXTENSIONLESS_FILES = new Set(['Rakefile', 'Gemfile', 'Guardfile', 'Vagrantfile', 'Brewfile']);
-
 /**
  * Map file extension to SupportedLanguage enum
  */
@@ -34,15 +31,6 @@ export const getLanguageFromFilename = (filename: string): SupportedLanguages |
       filename.endsWith('.php5') || filename.endsWith('.php8')) {
     return SupportedLanguages.PHP;
   }
-  // Ruby (extensions)
-  if (filename.endsWith('.rb') || filename.endsWith('.rake') || filename.endsWith('.gemspec')) {
-    return SupportedLanguages.Ruby;
-  }
-  // Ruby (extensionless files)
-  const basename = filename.split('/').pop() || filename;
-  if (RUBY_EXTENSIONLESS_FILES.has(basename)) {
-    return SupportedLanguages.Ruby;
-  }
   // Swift
   if (filename.endsWith('.swift')) return SupportedLanguages.Swift;
   return null;

gitnexus-web/src/core/kuzu/csv-generator.ts

@@ -1,5 +1,5 @@
 /**
- * CSV Generator for LadybugDB Hybrid Schema
+ * CSV Generator for KuzuDB Hybrid Schema
  * 
  * Generates separate CSV files for each node table and one relation CSV.
  * This enables efficient bulk loading via COPY FROM for hybrid schema.
@@ -18,10 +18,10 @@ import { NODE_TABLES, NodeTableName } from './schema';
 // ============================================================================
 
 /**
- * Sanitize string to ensure valid UTF-8 and safe CSV content for LadybugDB
+ * Sanitize string to ensure valid UTF-8 and safe CSV content for KuzuDB
  * Removes or replaces invalid characters that would break CSV parsing.
  * 
- * Critical: LadybugDB's CSV parser can misinterpret \r\n inside quoted fields.
+ * Critical: KuzuDB's CSV parser can misinterpret \r\n inside quoted fields.
  * We normalize all line endings to \n only.
  */
 const sanitizeUTF8 = (str: string): string => {
@@ -213,7 +213,7 @@ const generateCommunityCSV = (nodes: GraphNode[]): string => {
   for (const node of nodes) {
     if (node.label !== 'Community') continue;
     
-    // Handle keywords array - convert to LadybugDB array format
+    // Handle keywords array - convert to KuzuDB array format
     const keywords = (node.properties as any).keywords || [];
     const keywordsStr = `[${keywords.map((k: string) => `'${k.replace(/'/g, "''")}'`).join(',')}]`;
     
@@ -221,7 +221,7 @@ const generateCommunityCSV = (nodes: GraphNode[]): string => {
       escapeCSVField(node.id),
       escapeCSVField(node.properties.name || ''),  // label is stored in name
       escapeCSVField(node.properties.heuristicLabel || ''),
-      keywordsStr,  // Array format for LadybugDB
+      keywordsStr,  // Array format for KuzuDB
       escapeCSVField((node.properties as any).description || ''),
       escapeCSVField((node.properties as any).enrichedBy || 'heuristic'),
       escapeCSVNumber(node.properties.cohesion, 0),

gitnexus-web/src/core/kuzu/kuzu-adapter.ts

@@ -1,52 +1,51 @@
 /**
- * LadybugDB Adapter
- *
- * Manages the LadybugDB WASM instance for client-side graph database operations.
+ * KuzuDB Adapter
+ * 
+ * Manages the KuzuDB WASM instance for client-side graph database operations.
  * Uses the "Snapshot / Bulk Load" pattern with COPY FROM for performance.
- *
+ * 
  * Multi-table schema: separate tables for File, Function, Class, etc.
  */
 
 import { KnowledgeGraph } from '../graph/types';
-import {
-  NODE_TABLES,
+import { 
+  NODE_TABLES, 
   REL_TABLE_NAME,
-  SCHEMA_QUERIES,
+  SCHEMA_QUERIES, 
   EMBEDDING_TABLE_NAME,
   NodeTableName,
 } from './schema';
 import { generateAllCSVs } from './csv-generator';
-import { getQueryRows } from './query-result';
 
 // Holds the reference to the dynamically loaded module
-let lbug: any = null;
+let kuzu: any = null;
 let db: any = null;
 let conn: any = null;
 
 /**
- * Initialize LadybugDB WASM module and create in-memory database
+ * Initialize KuzuDB WASM module and create in-memory database
  */
-export const initLbug = async () => {
-  if (conn) return { db, conn, lbug };
+export const initKuzu = async () => {
+  if (conn) return { db, conn, kuzu };
 
   try {
-    if (import.meta.env.DEV) console.log('🚀 Initializing LadybugDB...');
+    if (import.meta.env.DEV) console.log('🚀 Initializing KuzuDB...');
 
     // 1. Dynamic Import (Fixes the "not a function" bundler issue)
-    const lbugModule = await import('@ladybugdb/wasm-core');
-
+    const kuzuModule = await import('kuzu-wasm');
+    
     // 2. Handle Vite/Webpack "default" wrapping
-    lbug = lbugModule.default || lbugModule;
+    kuzu = kuzuModule.default || kuzuModule;
 
     // 3. Initialize WASM
-    await lbug.init();
-
-    // 4. Create Database with 512MB buffer manager
+    await kuzu.init();
+    
+    // 4. Create Database with 512MB buffer pool
     const BUFFER_POOL_SIZE = 512 * 1024 * 1024; // 512MB
-    db = new lbug.Database(':memory:', BUFFER_POOL_SIZE);
-    conn = new lbug.Connection(db);
-
-    if (import.meta.env.DEV) console.log('✅ LadybugDB WASM Initialized');
+    db = new kuzu.Database(':memory:', BUFFER_POOL_SIZE);
+    conn = new kuzu.Connection(db);
+    
+    if (import.meta.env.DEV) console.log('✅ KuzuDB WASM Initialized');
 
     // 5. Initialize Schema (all node tables, then rel tables, then embedding table)
     for (const schemaQuery of SCHEMA_QUERIES) {
@@ -59,60 +58,60 @@ export const initLbug = async () => {
         }
       }
     }
+    
+    if (import.meta.env.DEV) console.log('✅ KuzuDB Multi-Table Schema Created');
 
-    if (import.meta.env.DEV) console.log('✅ LadybugDB Multi-Table Schema Created');
-
-    return { db, conn, lbug };
+    return { db, conn, kuzu };
   } catch (error) {
-    if (import.meta.env.DEV) console.error('❌ LadybugDB Initialization Failed:', error);
+    if (import.meta.env.DEV) console.error('❌ KuzuDB Initialization Failed:', error);
     throw error;
   }
 };
 
 /**
- * Load a KnowledgeGraph into LadybugDB using COPY FROM (bulk load)
+ * Load a KnowledgeGraph into KuzuDB using COPY FROM (bulk load)
  * Uses batched CSV writes and COPY statements for optimal performance
  */
-export const loadGraphToLbug = async (
-  graph: KnowledgeGraph,
+export const loadGraphToKuzu = async (
+  graph: KnowledgeGraph, 
   fileContents: Map<string, string>
 ) => {
-  const { conn, lbug } = await initLbug();
-
+  const { conn, kuzu } = await initKuzu();
+  
   try {
-    if (import.meta.env.DEV) console.log(`LadybugDB: Generating CSVs for ${graph.nodeCount} nodes...`);
-
+    if (import.meta.env.DEV) console.log(`KuzuDB: Generating CSVs for ${graph.nodeCount} nodes...`);
+    
     // 1. Generate all CSVs (per-table)
     const csvData = generateAllCSVs(graph, fileContents);
-
-    const fs = lbug.FS;
-
+    
+    const fs = kuzu.FS;
+    
     // 2. Write all node CSVs to virtual filesystem
     const nodeFiles: Array<{ table: NodeTableName; path: string }> = [];
     for (const [tableName, csv] of csvData.nodes.entries()) {
       // Skip empty CSVs (only header row)
       if (csv.split('\n').length <= 1) continue;
-
+      
       const path = `/${tableName.toLowerCase()}.csv`;
       try { await fs.unlink(path); } catch {}
       await fs.writeFile(path, csv);
       nodeFiles.push({ table: tableName, path });
     }
-
+    
     // 3. Parse relation CSV and prepare for INSERT (COPY FROM doesn't work with multi-pair tables)
     const relLines = csvData.relCSV.split('\n').slice(1).filter(line => line.trim());
     const relCount = relLines.length;
-
+    
     if (import.meta.env.DEV) {
-      console.log(`LadybugDB: Wrote ${nodeFiles.length} node CSVs, ${relCount} relations to insert`);
+      console.log(`KuzuDB: Wrote ${nodeFiles.length} node CSVs, ${relCount} relations to insert`);
     }
-
+    
     // 4. COPY all node tables (must complete before rels due to FK constraints)
     for (const { table, path } of nodeFiles) {
       const copyQuery = getCopyQuery(table, path);
       await conn.query(copyQuery);
     }
-
+    
     // 5. INSERT relations one by one (COPY doesn't work with multi-pair REL tables)
     // Build a set of valid table names for fast lookup
     const validTables = new Set<string>(NODE_TABLES as readonly string[]);
@@ -136,13 +135,13 @@ export const loadGraphToLbug = async (
         // Format: "from","to","type",confidence,"reason",step
         const match = line.match(/"([^"]*)","([^"]*)","([^"]*)",([0-9.]+),"([^"]*)",([0-9-]+)/);
         if (!match) continue;
-
+        
         const [, fromId, toId, relType, confidenceStr, reason, stepStr] = match;
 
         const fromLabel = getNodeLabel(fromId);
         const toLabel = getNodeLabel(toId);
 
-        // Skip relationships where either node's label doesn't have a table in LadybugDB
+        // Skip relationships where either node's label doesn't have a table in KuzuDB
         // Querying a non-existent table causes a fatal native crash
         if (!validTables.has(fromLabel) || !validTables.has(toLabel)) {
           skippedRels++;
@@ -151,7 +150,7 @@ export const loadGraphToLbug = async (
 
         const confidence = parseFloat(confidenceStr) || 1.0;
         const step = parseInt(stepStr) || 0;
-
+        
         const insertQuery = `
           MATCH (a:${escapeLabel(fromLabel)} {id: '${fromId.replace(/'/g, "''")}'}),
                 (b:${escapeLabel(toLabel)} {id: '${toId.replace(/'/g, "''")}'})
@@ -168,39 +167,38 @@ export const loadGraphToLbug = async (
           const toLabel = getNodeLabel(toId);
           const key = `${relType}:${fromLabel}->` + toLabel;
           skippedRelStats.set(key, (skippedRelStats.get(key) || 0) + 1);
-
+          
           if (import.meta.env.DEV) {
             console.warn(`⚠️ Skipped: ${key} | "${fromId}" → "${toId}" | ${err instanceof Error ? err.message : String(err)}`);
           }
         }
       }
     }
-
+    
     if (import.meta.env.DEV) {
-      console.log(`LadybugDB: Inserted ${insertedRels}/${relCount} relations`);
+      console.log(`KuzuDB: Inserted ${insertedRels}/${relCount} relations`);
       if (skippedRels > 0) {
         const topSkipped = Array.from(skippedRelStats.entries())
           .sort((a, b) => b[1] - a[1])
           .slice(0, 10);
-        console.warn(`LadybugDB: Skipped ${skippedRels}/${relCount} relations (top by kind/pair):`, topSkipped);
+        console.warn(`KuzuDB: Skipped ${skippedRels}/${relCount} relations (top by kind/pair):`, topSkipped);
       }
     }
-
+    
     // 6. Verify results
     let totalNodes = 0;
     for (const tableName of NODE_TABLES) {
       try {
         const countRes = await conn.query(`MATCH (n:${tableName}) RETURN count(n) AS cnt`);
-        const countRows = await getQueryRows(countRes);
-        const countRow = countRows[0];
+        const countRow = await countRes.getNext();
         const count = countRow ? (countRow.cnt ?? countRow[0] ?? 0) : 0;
         totalNodes += Number(count);
       } catch {
         // Table might be empty, skip
       }
     }
-
-    if (import.meta.env.DEV) console.log(`✅ LadybugDB Bulk Load Complete. Total nodes: ${totalNodes}, edges: ${insertedRels}`);
+    
+    if (import.meta.env.DEV) console.log(`✅ KuzuDB Bulk Load Complete. Total nodes: ${totalNodes}, edges: ${insertedRels}`);
 
     // 7. Cleanup CSV files
     for (const { path } of nodeFiles) {
@@ -210,12 +208,12 @@ export const loadGraphToLbug = async (
     return { success: true, count: totalNodes };
 
   } catch (error) {
-    if (import.meta.env.DEV) console.error('❌ LadybugDB Bulk Load Failed:', error);
+    if (import.meta.env.DEV) console.error('❌ KuzuDB Bulk Load Failed:', error);
     return { success: false, count: 0 };
   }
 };
 
-// LadybugDB default ESCAPE is '\' (backslash), but our CSV uses RFC 4180 escaping ("" for literal quotes).
+// KuzuDB default ESCAPE is '\' (backslash), but our CSV uses RFC 4180 escaping ("" for literal quotes).
 // Source code content is full of backslashes which confuse the auto-detection.
 // We MUST explicitly set ESCAPE='"' and disable auto_detect.
 const COPY_CSV_OPTS = `(HEADER=true, ESCAPE='"', DELIM=',', QUOTE='"', PARALLEL=false, auto_detect=false)`;
@@ -231,9 +229,6 @@ const escapeTableName = (table: string): string => {
   return BACKTICK_TABLES.has(table) ? `\`${table}\`` : table;
 };
 
-/** Tables with isExported column (TypeScript/JS-native types) */
-const TABLES_WITH_EXPORTED = new Set<string>(['Function', 'Class', 'Interface', 'Method', 'CodeElement']);
-
 /**
  * Get the COPY query for a node table with correct column mapping
  */
@@ -251,12 +246,8 @@ const getCopyQuery = (table: NodeTableName, path: string): string => {
   if (table === 'Process') {
     return `COPY ${t}(id, label, heuristicLabel, processType, stepCount, communities, entryPointId, terminalId) FROM "${path}" ${COPY_CSV_OPTS}`;
   }
-  // TypeScript/JS code element tables have isExported; multi-language tables do not
-  if (TABLES_WITH_EXPORTED.has(table)) {
-    return `COPY ${t}(id, name, filePath, startLine, endLine, isExported, content) FROM "${path}" ${COPY_CSV_OPTS}`;
-  }
-  // Multi-language tables (Struct, Impl, Trait, Macro, etc.)
-  return `COPY ${t}(id, name, filePath, startLine, endLine, content) FROM "${path}" ${COPY_CSV_OPTS}`;
+  // Code element tables (Function, Class, Interface, Method, CodeElement, and multi-language)
+  return `COPY ${t}(id, name, filePath, startLine, endLine, isExported, content) FROM "${path}" ${COPY_CSV_OPTS}`;
 };
 
 /**
@@ -265,12 +256,12 @@ const getCopyQuery = (table: NodeTableName, path: string): string => {
  */
 export const executeQuery = async (cypher: string): Promise<any[]> => {
   if (!conn) {
-    await initLbug();
+    await initKuzu();
   }
-
+  
   try {
     const result = await conn.query(cypher);
-
+    
     // Extract column names from RETURN clause
     const returnMatch = cypher.match(/RETURN\s+(.+?)(?:\s+ORDER|\s+LIMIT|\s+SKIP|\s*$)/is);
     let columnNames: string[] = [];
@@ -293,11 +284,12 @@ export const executeQuery = async (cypher: string): Promise<any[]> => {
         return col.replace(/[^a-zA-Z0-9_]/g, '_');
       });
     }
-
+    
     // Collect all rows
-    const allRows = await getQueryRows(result);
     const rows: any[] = [];
-    for (const row of allRows) {
+    while (await result.hasNext()) {
+      const row = await result.getNext();
+      
       // Convert tuple to named object if we have column names and row is array
       if (Array.isArray(row) && columnNames.length === row.length) {
         const namedRow: Record<string, any> = {};
@@ -310,7 +302,7 @@ export const executeQuery = async (cypher: string): Promise<any[]> => {
         rows.push(row);
       }
     }
-
+    
     return rows;
   } catch (error) {
     if (import.meta.env.DEV) console.error('Query execution failed:', error);
@@ -321,7 +313,7 @@ export const executeQuery = async (cypher: string): Promise<any[]> => {
 /**
  * Get database statistics
  */
-export const getLbugStats = async (): Promise<{ nodes: number; edges: number }> => {
+export const getKuzuStats = async (): Promise<{ nodes: number; edges: number }> => {
   if (!conn) {
     return { nodes: 0, edges: 0 };
   }
@@ -332,45 +324,43 @@ export const getLbugStats = async (): Promise<{ nodes: number; edges: number }>
     for (const tableName of NODE_TABLES) {
       try {
         const nodeResult = await conn.query(`MATCH (n:${tableName}) RETURN count(n) AS cnt`);
-        const nodeRows = await getQueryRows(nodeResult);
-        const nodeRow = nodeRows[0];
+        const nodeRow = await nodeResult.getNext();
         totalNodes += Number(nodeRow?.cnt ?? nodeRow?.[0] ?? 0);
       } catch {
         // Table might not exist or be empty
       }
     }
-
+    
     // Count edges from single relation table
     let totalEdges = 0;
     try {
       const edgeResult = await conn.query(`MATCH ()-[r:${REL_TABLE_NAME}]->() RETURN count(r) AS cnt`);
-      const edgeRows = await getQueryRows(edgeResult);
-      const edgeRow = edgeRows[0];
+      const edgeRow = await edgeResult.getNext();
       totalEdges = Number(edgeRow?.cnt ?? edgeRow?.[0] ?? 0);
     } catch {
       // Table might not exist or be empty
     }
-
+    
     return { nodes: totalNodes, edges: totalEdges };
   } catch (error) {
     if (import.meta.env.DEV) {
-      console.warn('Failed to get LadybugDB stats:', error);
+      console.warn('Failed to get Kuzu stats:', error);
     }
     return { nodes: 0, edges: 0 };
   }
 };
 
 /**
- * Check if LadybugDB is initialized and has data
+ * Check if KuzuDB is initialized and has data
  */
-export const isLbugReady = (): boolean => {
+export const isKuzuReady = (): boolean => {
   return conn !== null && db !== null;
 };
 
 /**
  * Close the database connection (cleanup)
  */
-export const closeLbug = async (): Promise<void> => {
+export const closeKuzu = async (): Promise<void> => {
   if (conn) {
     try {
       await conn.close();
@@ -383,7 +373,7 @@ export const closeLbug = async (): Promise<void> => {
     } catch {}
     db = null;
   }
-  lbug = null;
+  kuzu = null;
 };
 
 /**
@@ -397,20 +387,24 @@ export const executePrepared = async (
   params: Record<string, any>
 ): Promise<any[]> => {
   if (!conn) {
-    await initLbug();
+    await initKuzu();
   }
-
+  
   try {
     const stmt = await conn.prepare(cypher);
     if (!stmt.isSuccess()) {
       const errMsg = await stmt.getErrorMessage();
       throw new Error(`Prepare failed: ${errMsg}`);
     }
-
+    
     const result = await conn.execute(stmt, params);
-
-    const rows = await getQueryRows(result);
-
+    
+    const rows: any[] = [];
+    while (await result.hasNext()) {
+      const row = await result.getNext();
+      rows.push(row);
+    }
+    
     await stmt.close();
     return rows;
   } catch (error) {
@@ -427,22 +421,22 @@ export const executeWithReusedStatement = async (
   paramsList: Array<Record<string, any>>
 ): Promise<void> => {
   if (!conn) {
-    await initLbug();
+    await initKuzu();
   }
-
+  
   if (paramsList.length === 0) return;
-
+  
   const SUB_BATCH_SIZE = 4;
-
+  
   for (let i = 0; i < paramsList.length; i += SUB_BATCH_SIZE) {
     const subBatch = paramsList.slice(i, i + SUB_BATCH_SIZE);
-
+    
     const stmt = await conn.prepare(cypher);
     if (!stmt.isSuccess()) {
       const errMsg = await stmt.getErrorMessage();
       throw new Error(`Prepare failed: ${errMsg}`);
     }
-
+    
     try {
       for (const params of subBatch) {
         await conn.execute(stmt, params);
@@ -450,7 +444,7 @@ export const executeWithReusedStatement = async (
     } finally {
       await stmt.close();
     }
-
+    
     if (i + SUB_BATCH_SIZE < paramsList.length) {
       await new Promise(r => setTimeout(r, 0));
     }
@@ -462,67 +456,65 @@ export const executeWithReusedStatement = async (
  */
 export const testArrayParams = async (): Promise<{ success: boolean; error?: string }> => {
   if (!conn) {
-    await initLbug();
+    await initKuzu();
   }
-
+  
   try {
     const testEmbedding = new Array(384).fill(0).map((_, i) => i / 384);
-
+    
     // Get any node ID to test with (try File first, then others)
     let testNodeId: string | null = null;
     for (const tableName of NODE_TABLES) {
       try {
         const nodeResult = await conn.query(`MATCH (n:${tableName}) RETURN n.id AS id LIMIT 1`);
-        const nodeRows = await getQueryRows(nodeResult);
-        const nodeRow = nodeRows[0];
+        const nodeRow = await nodeResult.getNext();
         if (nodeRow) {
           testNodeId = nodeRow.id ?? nodeRow[0];
           break;
         }
       } catch {}
     }
-
+    
     if (!testNodeId) {
       return { success: false, error: 'No nodes found to test with' };
     }
-
+    
     if (import.meta.env.DEV) {
       console.log('🧪 Testing array params with node:', testNodeId);
     }
-
+    
     // First create an embedding entry
     const createQuery = `CREATE (e:${EMBEDDING_TABLE_NAME} {nodeId: $nodeId, embedding: $embedding})`;
     const stmt = await conn.prepare(createQuery);
-
+    
     if (!stmt.isSuccess()) {
       const errMsg = await stmt.getErrorMessage();
       return { success: false, error: `Prepare failed: ${errMsg}` };
     }
-
+    
     await conn.execute(stmt, {
       nodeId: testNodeId,
       embedding: testEmbedding,
     });
-
+    
     await stmt.close();
-
+    
     // Verify it was stored
     const verifyResult = await conn.query(
       `MATCH (e:${EMBEDDING_TABLE_NAME} {nodeId: '${testNodeId}'}) RETURN e.embedding AS emb`
     );
-    const verifyRows = await getQueryRows(verifyResult);
-    const verifyRow = verifyRows[0];
+    const verifyRow = await verifyResult.getNext();
     const storedEmb = verifyRow?.emb ?? verifyRow?.[0];
-
+    
     if (storedEmb && Array.isArray(storedEmb) && storedEmb.length === 384) {
       if (import.meta.env.DEV) {
         console.log('✅ Array params WORK! Stored embedding length:', storedEmb.length);
       }
       return { success: true };
     } else {
-      return {
-        success: false,
-        error: `Embedding not stored correctly. Got: ${typeof storedEmb}, length: ${storedEmb?.length}`
+      return { 
+        success: false, 
+        error: `Embedding not stored correctly. Got: ${typeof storedEmb}, length: ${storedEmb?.length}` 
       };
     }
   } catch (error) {

gitnexus-web/src/core/kuzu/schema.ts

@@ -1,5 +1,5 @@
 /**
- * LadybugDB Schema Definitions
+ * KuzuDB Schema Definitions
  * 
  * Hybrid Schema:
  * - Separate node tables for each code element type (File, Function, Class, etc.)

gitnexus-web/src/core/lbug/query-result.test.ts

@@ -1,41 +0,0 @@
-import { describe, expect, it, vi } from 'vitest';
-
-import { getQueryRows } from './query-result';
-
-describe('getQueryRows', () => {
-  it('prefers getAllObjects when available', async () => {
-    const rows = [{ name: 'foo' }];
-    const getAllObjects = vi.fn().mockResolvedValue(rows);
-    const getAllRows = vi.fn().mockResolvedValue([{ name: 'bar' }]);
-    const getAll = vi.fn().mockResolvedValue([['baz']]);
-
-    await expect(getQueryRows({ getAllObjects, getAllRows, getAll })).resolves.toEqual(rows);
-
-    expect(getAllObjects).toHaveBeenCalledTimes(1);
-    expect(getAllRows).not.toHaveBeenCalled();
-    expect(getAll).not.toHaveBeenCalled();
-  });
-
-  it('falls back to getAllRows when getAllObjects is absent', async () => {
-    const rows = [{ name: 'bar' }];
-    const getAllRows = vi.fn().mockResolvedValue(rows);
-    const getAll = vi.fn().mockResolvedValue([['baz']]);
-
-    await expect(getQueryRows({ getAllRows, getAll })).resolves.toEqual(rows);
-
-    expect(getAllRows).toHaveBeenCalledTimes(1);
-    expect(getAll).not.toHaveBeenCalled();
-  });
-
-  it('falls back to getAll as a final fallback', async () => {
-    const rows = [['baz']];
-    const getAll = vi.fn().mockResolvedValue(rows);
-
-    await expect(getQueryRows({ getAll })).resolves.toEqual(rows);
-    expect(getAll).toHaveBeenCalledTimes(1);
-  });
-
-  it('throws when no supported query API is exposed', async () => {
-    await expect(getQueryRows({})).rejects.toThrow('Unsupported LadybugDB QueryResult shape');
-  });
-});

gitnexus-web/src/core/lbug/query-result.ts

@@ -1,21 +0,0 @@
-export const getQueryRows = async (result: unknown): Promise<any[]> => {
-  if (!result || typeof result !== 'object') return [];
-
-  const queryResult = result as {
-    getAllObjects?: () => Promise<any[]>;
-    getAllRows?: () => Promise<any[]>;
-    getAll?: () => Promise<any[]>;
-  };
-
-  if (typeof queryResult.getAllObjects === 'function') {
-    return await queryResult.getAllObjects();
-  }
-  if (typeof queryResult.getAllRows === 'function') {
-    return await queryResult.getAllRows();
-  }
-  if (typeof queryResult.getAll === 'function') {
-    return await queryResult.getAll();
-  }
-
-  throw new Error('Unsupported LadybugDB QueryResult shape');
-};

gitnexus-web/src/core/llm/agent.ts

@@ -13,15 +13,14 @@ import { ChatAnthropic } from '@langchain/anthropic';
 import { ChatOllama } from '@langchain/ollama';
 import type { BaseChatModel } from '@langchain/core/language_models/chat_models';
 import { createGraphRAGTools } from './tools';
-import type {
-  ProviderConfig,
+import type { 
+  ProviderConfig, 
   OpenAIConfig,
-  AzureOpenAIConfig,
+  AzureOpenAIConfig, 
   GeminiConfig,
   AnthropicConfig,
   OllamaConfig,
   OpenRouterConfig,
-  MiniMaxConfig,
   AgentStreamChunk,
 } from './types';
 import { 
@@ -198,7 +197,7 @@ export const createChatModel = (config: ProviderConfig): BaseChatModel => {
     
     case 'openrouter': {
       const openRouterConfig = config as OpenRouterConfig;
-
+      
       // Debug logging
       if (import.meta.env.DEV) {
         console.log('🌐 OpenRouter config:', {
@@ -208,11 +207,11 @@ export const createChatModel = (config: ProviderConfig): BaseChatModel => {
           baseUrl: openRouterConfig.baseUrl,
         });
       }
-
+      
       if (!openRouterConfig.apiKey || openRouterConfig.apiKey.trim() === '') {
         throw new Error('OpenRouter API key is required but was not provided');
       }
-
+      
       return new ChatOpenAI({
         openAIApiKey: openRouterConfig.apiKey,
         apiKey: openRouterConfig.apiKey, // Fallback for some versions
@@ -226,26 +225,7 @@ export const createChatModel = (config: ProviderConfig): BaseChatModel => {
         streaming: true,
       });
     }
-
-    case 'minimax': {
-      const minimaxConfig = config as MiniMaxConfig;
-
-      if (!minimaxConfig.apiKey || minimaxConfig.apiKey.trim() === '') {
-        throw new Error('MiniMax API key is required but was not provided');
-      }
-
-      return new ChatAnthropic({
-        anthropicApiKey: minimaxConfig.apiKey,
-        model: minimaxConfig.model,
-        temperature: minimaxConfig.temperature ?? 0.1,
-        maxTokens: minimaxConfig.maxTokens ?? 8192,
-        streaming: true,
-        clientOptions: {
-          baseURL: 'https://api.minimax.io/anthropic',
-        },
-      });
-    }
-
+    
     default:
       throw new Error(`Unsupported provider: ${(config as any).provider}`);
   }

gitnexus-web/src/core/llm/settings-service.ts

@@ -5,9 +5,9 @@
  * All API keys are stored locally - never sent to any server except the LLM provider.
  */
 
-import {
-  LLMSettings,
-  DEFAULT_LLM_SETTINGS,
+import { 
+  LLMSettings, 
+  DEFAULT_LLM_SETTINGS, 
   LLMProvider,
   OpenAIConfig,
   AzureOpenAIConfig,
@@ -15,7 +15,6 @@ import {
   AnthropicConfig,
   OllamaConfig,
   OpenRouterConfig,
-  MiniMaxConfig,
   ProviderConfig,
 } from './types';
 
@@ -61,10 +60,6 @@ export const loadSettings = (): LLMSettings => {
         ...DEFAULT_LLM_SETTINGS.openrouter,
         ...parsed.openrouter,
       },
-      minimax: {
-        ...DEFAULT_LLM_SETTINGS.minimax,
-        ...parsed.minimax,
-      },
     };
   } catch (error) {
     console.warn('Failed to load LLM settings:', error);
@@ -94,7 +89,6 @@ export const updateProviderSettings = <T extends LLMProvider>(
     T extends 'gemini' ? Partial<Omit<GeminiConfig, 'provider'>> :
     T extends 'anthropic' ? Partial<Omit<AnthropicConfig, 'provider'>> :
     T extends 'ollama' ? Partial<Omit<OllamaConfig, 'provider'>> :
-    T extends 'minimax' ? Partial<Omit<MiniMaxConfig, 'provider'>> :
     never
   >
 ): LLMSettings => {
@@ -168,17 +162,6 @@ export const updateProviderSettings = <T extends LLMProvider>(
       saveSettings(updated);
       return updated;
     }
-    case 'minimax': {
-      const updated: LLMSettings = {
-        ...current,
-        minimax: {
-          ...(current.minimax ?? {}),
-          ...(updates as Partial<Omit<MiniMaxConfig, 'provider'>>),
-        },
-      };
-      saveSettings(updated);
-      return updated;
-    }
     default: {
       // Should be unreachable due to T extends LLMProvider, but keep a safe fallback
       const updated: LLMSettings = { ...current };
@@ -262,16 +245,7 @@ export const getActiveProviderConfig = (): ProviderConfig | null => {
         temperature: settings.openrouter.temperature,
         maxTokens: settings.openrouter.maxTokens,
       } as OpenRouterConfig;
-
-    case 'minimax':
-      if (!settings.minimax?.apiKey) {
-        return null;
-      }
-      return {
-        provider: 'minimax',
-        ...settings.minimax,
-      } as MiniMaxConfig;
-
+      
     default:
       return null;
   }
@@ -308,8 +282,6 @@ export const getProviderDisplayName = (provider: LLMProvider): string => {
       return 'Ollama (Local)';
     case 'openrouter':
       return 'OpenRouter';
-    case 'minimax':
-      return 'MiniMax';
     default:
       return provider;
   }
@@ -331,8 +303,6 @@ export const getAvailableModels = (provider: LLMProvider): string[] => {
       return ['claude-sonnet-4-20250514', 'claude-3-5-sonnet-20241022', 'claude-3-5-haiku-20241022', 'claude-3-opus-20240229'];
     case 'ollama':
       return ['llama3.2', 'llama3.1', 'mistral', 'codellama', 'deepseek-coder'];
-    case 'minimax':
-      return ['MiniMax-M2.5', 'MiniMax-M2.5-highspeed'];
     default:
       return [];
   }

gitnexus-web/src/core/llm/tools.ts

@@ -17,7 +17,7 @@ import { z } from 'zod';
 import { WebGPUNotAvailableError, embedText, embeddingToArray, initEmbedder, isEmbedderReady } from '../embeddings/embedder';
 
 /**
- * Tool factory - creates tools bound to the LadybugDB query functions
+ * Tool factory - creates tools bound to the KuzuDB query functions
  */
 export const createGraphRAGTools = (
   executeQuery: (cypher: string) => Promise<any[]>,
@@ -975,7 +975,7 @@ MATCH (n:Function {id: emb.nodeId}) RETURN n`,
       // For code elements (Function, Class, etc.), use the direct id
       const isFileTarget = targetType === 'File';
       
-      // Query each depth level separately (LadybugDB doesn't support list comprehensions on paths)
+      // Query each depth level separately (KuzuDB doesn't support list comprehensions on paths)
       // For depth 1: direct connections only
       // For depth 2+: chain multiple single-hop queries
       const depthQueries: Promise<any[]>[] = [];

gitnexus-web/src/core/llm/types.ts

@@ -8,7 +8,7 @@
 /**
  * Supported LLM providers
  */
-export type LLMProvider = 'openai' | 'azure-openai' | 'gemini' | 'anthropic' | 'ollama' | 'openrouter' | 'minimax';
+export type LLMProvider = 'openai' | 'azure-openai' | 'gemini' | 'anthropic' | 'ollama' | 'openrouter';
 
 /**
  * Base configuration shared by all providers
@@ -78,19 +78,10 @@ export interface OpenRouterConfig extends BaseProviderConfig {
   baseUrl?: string;  // defaults to https://openrouter.ai/api/v1
 }
 
-/**
- * MiniMax configuration (Anthropic-compatible API)
- */
-export interface MiniMaxConfig extends BaseProviderConfig {
-  provider: 'minimax';
-  apiKey: string;
-  model: string;  // e.g., 'MiniMax-M2.5', 'MiniMax-M2.5-highspeed'
-}
-
 /**
  * Union type for all provider configurations
  */
-export type ProviderConfig = OpenAIConfig | AzureOpenAIConfig | GeminiConfig | AnthropicConfig | OllamaConfig | OpenRouterConfig | MiniMaxConfig;
+export type ProviderConfig = OpenAIConfig | AzureOpenAIConfig | GeminiConfig | AnthropicConfig | OllamaConfig | OpenRouterConfig;
 
 /**
  * Stored settings (what goes to localStorage)
@@ -107,7 +98,6 @@ export interface LLMSettings {
   anthropic?: Partial<Omit<AnthropicConfig, 'provider'>>;
   ollama?: Partial<Omit<OllamaConfig, 'provider'>>;
   openrouter?: Partial<Omit<OpenRouterConfig, 'provider'>>;
-  minimax?: Partial<Omit<MiniMaxConfig, 'provider'>>;
 
   // Intelligent Clustering Settings
   intelligentClustering: boolean;
@@ -158,11 +148,6 @@ export const DEFAULT_LLM_SETTINGS: LLMSettings = {
     baseUrl: 'https://openrouter.ai/api/v1',
     temperature: 0.1,
   },
-  minimax: {
-    apiKey: '',
-    model: 'MiniMax-M2.5',
-    temperature: 0.1,
-  },
 };
 
 /**
@@ -239,7 +224,7 @@ export interface AgentStep {
  * Graph schema information for LLM context
  */
 export const GRAPH_SCHEMA_DESCRIPTION = `
-LADYBUG GRAPH DATABASE SCHEMA (Multi-Table):
+KUZU GRAPH DATABASE SCHEMA (Multi-Table):
 
 NODE TABLES:
 1. File - Source files

gitnexus-web/src/core/tree-sitter/parser-loader.ts

@@ -40,8 +40,6 @@ const getWasmPath = (language: SupportedLanguages, filePath?: string): string =>
         [SupportedLanguages.Go]: '/wasm/go/tree-sitter-go.wasm',
         [SupportedLanguages.Rust]: '/wasm/rust/tree-sitter-rust.wasm',
         [SupportedLanguages.PHP]: '/wasm/php/tree-sitter-php.wasm',
-        [SupportedLanguages.Ruby]: '/wasm/ruby/tree-sitter-ruby.wasm',
-        [SupportedLanguages.Kotlin]: '', // Kotlin WASM parser not yet available for web
         [SupportedLanguages.Swift]: '/wasm/swift/tree-sitter-swift.wasm',
     };
     

gitnexus-web/src/hooks/useAppState.tsx

@@ -1,6 +1,6 @@
 import { createContext, useContext, useState, useCallback, useRef, useEffect, ReactNode } from 'react';
 import * as Comlink from 'comlink';
-import { KnowledgeGraph, GraphNode, GraphRelationship, NodeLabel } from '../core/graph/types';
+import { KnowledgeGraph, GraphNode, NodeLabel } from '../core/graph/types';
 import { PipelineProgress, PipelineResult, deserializePipelineResult } from '../types/pipeline';
 import { createKnowledgeGraph } from '../core/graph/graph';
 import { DEFAULT_VISIBLE_LABELS } from '../lib/constants';
@@ -95,7 +95,6 @@ interface AppState {
   isAIHighlightsEnabled: boolean;
   toggleAIHighlights: () => void;
   clearAIToolHighlights: () => void;
-  clearAICitationHighlights: () => void;
   clearBlastRadius: () => void;
   queryResult: QueryResult | null;
   setQueryResult: (result: QueryResult | null) => void;
@@ -126,7 +125,6 @@ interface AppState {
   runPipelineFromFiles: (files: FileEntry[], onProgress: (p: PipelineProgress) => void, clusteringConfig?: ProviderConfig) => Promise<PipelineResult>;
   runQuery: (cypher: string) => Promise<any[]>;
   isDatabaseReady: () => Promise<boolean>;
-  loadServerGraph: (nodes: GraphNode[], relationships: GraphRelationship[], fileContents: Record<string, string>) => Promise<void>;
 
   // Embedding state
   embeddingStatus: EmbeddingStatus;
@@ -145,9 +143,7 @@ interface AppState {
   llmSettings: LLMSettings;
   updateLLMSettings: (updates: Partial<LLMSettings>) => void;
   isSettingsPanelOpen: boolean;
-  isHelpDialogBoxOpen: boolean;
   setSettingsPanelOpen: (open: boolean) => void;
-  setHelpDialogBoxOpen: (open: boolean) => void;
   isAgentReady: boolean;
   isAgentInitializing: boolean;
   agentError: string | null;
@@ -229,10 +225,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     setAIToolHighlightedNodeIds(new Set());
   }, []);
 
-  const clearAICitationHighlights = useCallback(() => {
-    setAICitationHighlightedNodeIds(new Set());
-  }, []);
-
   const clearBlastRadius = useCallback(() => {
     setBlastRadiusNodeIds(new Set());
   }, []);
@@ -298,7 +290,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
   // LLM/Agent state
   const [llmSettings, setLLMSettings] = useState<LLMSettings>(loadSettings);
   const [isSettingsPanelOpen, setSettingsPanelOpen] = useState(false);
-  const [isHelpDialogBoxOpen, setHelpDialogBoxOpen] = useState(false);
   const [isAgentReady, setIsAgentReady] = useState(false);
   const [isAgentInitializing, setIsAgentInitializing] = useState(false);
   const [agentError, setAgentError] = useState<string | null>(null);
@@ -491,16 +482,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     }
   }, []);
 
-  const loadServerGraph = useCallback(async (
-    nodes: GraphNode[],
-    relationships: GraphRelationship[],
-    fileContents: Record<string, string>
-  ): Promise<void> => {
-    const api = apiRef.current;
-    if (!api) throw new Error('Worker not initialized');
-    await api.loadServerGraph(nodes, relationships, fileContents);
-  }, []);
-
   // Embedding methods
   const startEmbeddings = useCallback(async (forceDevice?: 'webgpu' | 'wasm'): Promise<void> => {
     const api = apiRef.current;
@@ -998,13 +979,10 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     setProgress({ phase: 'extracting', percent: 0, message: 'Switching repository...', detail: `Loading ${repoName}` });
     setViewMode('loading');
 
-    setIsAgentReady(false);
-
     // Clear stale graph state from previous repo (highlights, selections, blast radius)
     // Without this, sigma reducers dim ALL nodes/edges because old node IDs don't match
     setHighlightedNodeIds(new Set());
     clearAIToolHighlights();
-    clearAICitationHighlights();
     clearBlastRadius();
     setSelectedNode(null);
     setQueryResult(null);
@@ -1039,29 +1017,17 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
       for (const [p, c] of Object.entries(result.fileContents)) fileMap.set(p, c);
       setFileContents(fileMap);
 
-      // Load graph into LadybugDB for Nexus AI queries, then init agent
-      try {
-        await loadServerGraph(result.nodes, result.relationships, result.fileContents);
-        if (getActiveProviderConfig()) {
-          await initializeAgent(pName);
+      setViewMode('exploring');
+
+      if (getActiveProviderConfig()) initializeAgent(pName);
+
+      startEmbeddings().catch((err) => {
+        if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
+          startEmbeddings('wasm').catch(console.warn);
+        } else {
+          console.warn('Embeddings auto-start failed:', err);
         }
-        setViewMode('exploring');
-        startEmbeddings().catch((err) => {
-          if (err?.name === 'WebGPUNotAvailableError' || err?.message?.includes('WebGPU')) {
-            startEmbeddings('wasm').catch(console.warn);
-          } else {
-            console.warn('Embeddings auto-start failed:', err);
-          }
-        });
-        setProgress(null);
-      } catch (err) {
-        console.warn('Failed to load graph into LadybugDB:', err);
-        setIsAgentReady(false);
-        await apiRef.current?.disposeAgent();
-        setAgentError('Failed to load graph into LadybugDB');
-        setViewMode('exploring');
-        setProgress(null);
-      }
+      });
     } catch (err) {
       console.error('Repo switch failed:', err);
       setProgress({
@@ -1069,11 +1035,9 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
         message: 'Failed to switch repository',
         detail: err instanceof Error ? err.message : 'Unknown error',
       });
-      setIsAgentReady(false);
-      await apiRef.current?.disposeAgent();
       setTimeout(() => { setViewMode('exploring'); setProgress(null); }, 3000);
     }
-  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, loadServerGraph, initializeAgent, startEmbeddings, setHighlightedNodeIds, clearAIToolHighlights, clearAICitationHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
+  }, [serverBaseUrl, setProgress, setViewMode, setProjectName, setGraph, setFileContents, initializeAgent, startEmbeddings, setHighlightedNodeIds, clearAIToolHighlights, clearBlastRadius, setSelectedNode, setQueryResult, setCodeReferences, setCodePanelOpen, setCodeReferenceFocus]);
 
   const removeCodeReference = useCallback((id: string) => {
     setCodeReferences(prev => {
@@ -1156,7 +1120,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     isAIHighlightsEnabled,
     toggleAIHighlights,
     clearAIToolHighlights,
-    clearAICitationHighlights,
     clearBlastRadius,
     queryResult,
     setQueryResult,
@@ -1179,7 +1142,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     runPipelineFromFiles,
     runQuery,
     isDatabaseReady,
-    loadServerGraph,
     // Embedding state and methods
     embeddingStatus,
     embeddingProgress,
@@ -1194,8 +1156,6 @@ export const AppStateProvider = ({ children }: { children: ReactNode }) => {
     updateLLMSettings,
     isSettingsPanelOpen,
     setSettingsPanelOpen,
-    isHelpDialogBoxOpen,
-    setHelpDialogBoxOpen,
     isAgentReady,
     isAgentInitializing,
     agentError,

gitnexus-web/src/types/kuzu-wasm.d.ts

@@ -1,37 +1,28 @@
-declare module '@ladybugdb/wasm-core' {
+declare module 'kuzu-wasm' {
   export function init(): Promise<void>;
   export class Database {
-    constructor(path: string, bufferPoolSize?: number);
+    constructor(path: string);
     close(): Promise<void>;
   }
   export class Connection {
     constructor(db: Database);
     query(cypher: string): Promise<QueryResult>;
-    prepare(cypher: string): Promise<PreparedStatement>;
-    execute(stmt: PreparedStatement, params?: Record<string, any>): Promise<QueryResult>;
     close(): Promise<void>;
   }
   export interface QueryResult {
-    getAll?(): Promise<any[]>;
-    getAllRows?(): Promise<any[]>;
-    getAllObjects?(): Promise<any[]>;
     hasNext(): Promise<boolean>;
     getNext(): Promise<any>;
   }
-  export interface PreparedStatement {
-    isSuccess(): boolean;
-    getErrorMessage(): Promise<string>;
-    close(): Promise<void>;
-  }
   export const FS: {
     writeFile(path: string, data: string): Promise<void>;
     unlink(path: string): Promise<void>;
   };
-  const lbug: {
+  const kuzu: {
     init: typeof init;
     Database: typeof Database;
     Connection: typeof Connection;
     FS: typeof FS;
   };
-  export default lbug;
+  export default kuzu;
 }
+

gitnexus-web/src/workers/ingestion.worker.ts

@@ -1,7 +1,5 @@
 import * as Comlink from 'comlink';
 import { runIngestionPipeline, runPipelineFromFiles } from '../core/ingestion/pipeline';
-import { createKnowledgeGraph } from '../core/graph/graph';
-import type { GraphNode, GraphRelationship } from '../core/graph/types';
 import { PipelineProgress, SerializablePipelineResult, serializePipelineResult } from '../types/pipeline';
 import { FileEntry } from '../services/zip';
 import {
@@ -19,83 +17,28 @@ import { enrichClustersBatch, ClusterMemberInfo, ClusterEnrichment } from '../co
 import { CommunityNode } from '../core/ingestion/community-processor';
 import { PipelineResult } from '../types/pipeline';
 import { buildCodebaseContext, type CodebaseContext } from '../core/llm/context-builder';
-import {
-  buildBM25Index,
-  searchBM25,
-  isBM25Ready,
+import { 
+  buildBM25Index, 
+  searchBM25, 
+  isBM25Ready, 
   getBM25Stats,
   mergeWithRRF,
   type HybridSearchResult,
 } from '../core/search';
 
-// Lazy import for LadybugDB to avoid breaking worker if SharedArrayBuffer unavailable
-let lbugAdapter: typeof import('../core/lbug/lbug-adapter') | null = null;
-const getLbugAdapter = async () => {
-  if (!lbugAdapter) {
-    lbugAdapter = await import('../core/lbug/lbug-adapter');
+// Lazy import for Kuzu to avoid breaking worker if SharedArrayBuffer unavailable
+let kuzuAdapter: typeof import('../core/kuzu/kuzu-adapter') | null = null;
+const getKuzuAdapter = async () => {
+  if (!kuzuAdapter) {
+    kuzuAdapter = await import('../core/kuzu/kuzu-adapter');
   }
-  return lbugAdapter;
+  return kuzuAdapter;
 };
 
 // Embedding state
 let embeddingProgress: EmbeddingProgress | null = null;
 let isEmbeddingComplete = false;
 
-/**
- * Shared post-pipeline logic: store results, build BM25 index, load LadybugDB,
- * and queue enrichment config. Used by both runPipeline and runPipelineFromFiles.
- */
-const finalizePipeline = async (
-  result: PipelineResult,
-  onProgress: (progress: PipelineProgress) => void,
-  clusteringConfig?: ProviderConfig
-): Promise<SerializablePipelineResult> => {
-  currentGraphResult = result;
-
-  // Store file contents for grep/read tools (full content, not truncated)
-  storedFileContents = result.fileContents;
-
-  // Build BM25 index for keyword search (instant, ~100ms)
-  const bm25DocCount = buildBM25Index(storedFileContents);
-  if (import.meta.env.DEV) {
-    console.log(`🔍 BM25 index built: ${bm25DocCount} documents`);
-  }
-
-  // Load graph into LadybugDB for querying (optional - gracefully degrades)
-  try {
-    onProgress({
-      phase: 'complete',
-      percent: 98,
-      message: 'Loading into LadybugDB...',
-      stats: {
-        filesProcessed: result.graph.nodeCount,
-        totalFiles: result.graph.nodeCount,
-        nodesCreated: result.graph.nodeCount,
-      },
-    });
-
-    const lbug = await getLbugAdapter();
-    await lbug.loadGraphToLbug(result.graph, result.fileContents);
-
-    if (import.meta.env.DEV) {
-      const stats = await lbug.getLbugStats();
-      console.log('LadybugDB loaded:', stats);
-      console.log('📁 Stored', storedFileContents.size, 'files for grep/read tools');
-    }
-  } catch {
-    // LadybugDB is optional - silently continue without it
-  }
-
-  // Store clustering config for background enrichment (runs after graph loads)
-  if (clusteringConfig) {
-    pendingEnrichmentConfig = clusteringConfig;
-    console.log('📋 Clustering config saved for background enrichment');
-  }
-
-  // Convert to serializable format for transfer back to main thread
-  return serializePipelineResult(result);
-};
-
 // File contents state - stores full file contents for grep/read tools
 let storedFileContents: Map<string, string> = new Map();
 
@@ -214,70 +157,67 @@ const workerApi = {
     onProgress: (progress: PipelineProgress) => void,
     clusteringConfig?: ProviderConfig
   ): Promise<SerializablePipelineResult> {
+    // Debug logging
     console.log('🔧 runPipeline called with clusteringConfig:', !!clusteringConfig);
+    // Run the actual pipeline
     const result = await runIngestionPipeline(file, onProgress);
-    return finalizePipeline(result, onProgress, clusteringConfig);
-  },
-
-  /**
-   * Load a pre-built graph from the server into LadybugDB.
-   * Called when connecting via server (bypasses the WASM ingestion pipeline).
-   */
-  async loadServerGraph(
-    nodes: GraphNode[],
-    relationships: GraphRelationship[],
-    fileContents: Record<string, string>
-  ): Promise<void> {
-    const graph = createKnowledgeGraph();
-    for (const node of nodes) graph.addNode(node);
-    for (const rel of relationships) graph.addRelationship(rel);
-
-    const fileMap = new Map<string, string>();
-    for (const [path, content] of Object.entries(fileContents)) {
-      fileMap.set(path, content);
+    currentGraphResult = result;
+    
+    // Store file contents for grep/read tools (full content, not truncated)
+    storedFileContents = result.fileContents;
+    
+    // Build BM25 index for keyword search (instant, ~100ms)
+    const bm25DocCount = buildBM25Index(storedFileContents);
+    if (import.meta.env.DEV) {
+      console.log(`🔍 BM25 index built: ${bm25DocCount} documents`);
     }
-
-    // Replace (not accumulate) stored file contents for grep/read tools
-    storedFileContents = fileMap;
-
-    // Track graph result for downstream APIs (enrichCommunities, etc.)
-    currentGraphResult = { graph, fileContents: fileMap };
-    isEmbeddingComplete = false;
-    embeddingProgress = null;
-
-    // Load graph into LadybugDB and build BM25 index (optional - gracefully degrades)
+    
+    // Load graph into KuzuDB for querying (optional - gracefully degrades)
     try {
-      const lbug = await getLbugAdapter();
-      await lbug.loadGraphToLbug(graph, fileMap);
-
-      // Build BM25 index for text search
-      buildBM25Index(fileMap);
-
+      onProgress({
+        phase: 'complete',
+        percent: 98,
+        message: 'Loading into KuzuDB...',
+        stats: {
+          filesProcessed: result.graph.nodeCount,
+          totalFiles: result.graph.nodeCount,
+          nodesCreated: result.graph.nodeCount,
+        },
+      });
+      
+      const kuzu = await getKuzuAdapter();
+      await kuzu.loadGraphToKuzu(result.graph, result.fileContents);
+      
       if (import.meta.env.DEV) {
-        const stats = await lbug.getLbugStats();
-        console.log('LadybugDB loaded from server:', stats);
+        const stats = await kuzu.getKuzuStats();
+        console.log('KuzuDB loaded:', stats);
         console.log('📁 Stored', storedFileContents.size, 'files for grep/read tools');
       }
-    } catch (err) {
-      if (import.meta.env.DEV) {
-        console.warn('LadybugDB load failed (non-fatal, continuing without it):', err);
-      }
-      // Still build BM25 index even if LadybugDB fails
-      buildBM25Index(fileMap);
+    } catch {
+      // KuzuDB is optional - silently continue without it
     }
+    
+    // Store clustering config for background enrichment (runs after graph loads)
+    if (clusteringConfig) {
+      pendingEnrichmentConfig = clusteringConfig;
+      console.log('📋 Clustering config saved for background enrichment');
+    }
+    
+    // Convert to serializable format for transfer back to main thread
+    return serializePipelineResult(result);
   },
 
   /**
-   * Execute a Cypher query against the LadybugDB database
+   * Execute a Cypher query against the KuzuDB database
    * @param cypher - The Cypher query string
    * @returns Query results as an array of objects
    */
   async runQuery(cypher: string): Promise<any[]> {
-    const lbug = await getLbugAdapter();
-    if (!lbug.isLbugReady()) {
+    const kuzu = await getKuzuAdapter();
+    if (!kuzu.isKuzuReady()) {
       throw new Error('Database not ready. Please load a repository first.');
     }
-    return lbug.executeQuery(cypher);
+    return kuzu.executeQuery(cypher);
   },
 
   /**
@@ -285,8 +225,8 @@ const workerApi = {
    */
   async isReady(): Promise<boolean> {
     try {
-      const lbug = await getLbugAdapter();
-      return lbug.isLbugReady();
+      const kuzu = await getKuzuAdapter();
+      return kuzu.isKuzuReady();
     } catch {
       return false;
     }
@@ -297,8 +237,8 @@ const workerApi = {
    */
   async getStats(): Promise<{ nodes: number; edges: number }> {
     try {
-      const lbug = await getLbugAdapter();
-      return lbug.getLbugStats();
+      const kuzu = await getKuzuAdapter();
+      return kuzu.getKuzuStats();
     } catch {
       return { nodes: 0, edges: 0 };
     }
@@ -323,8 +263,52 @@ const workerApi = {
       stats: { filesProcessed: 0, totalFiles: files.length, nodesCreated: 0 },
     });
 
+    // Run the pipeline
     const result = await runPipelineFromFiles(files, onProgress);
-    return finalizePipeline(result, onProgress, clusteringConfig);
+    currentGraphResult = result;
+    
+    // Store file contents for grep/read tools (full content, not truncated)
+    storedFileContents = result.fileContents;
+    
+    // Build BM25 index for keyword search (instant, ~100ms)
+    const bm25DocCount = buildBM25Index(storedFileContents);
+    if (import.meta.env.DEV) {
+      console.log(`🔍 BM25 index built: ${bm25DocCount} documents`);
+    }
+    
+    // Load graph into KuzuDB for querying (optional - gracefully degrades)
+    try {
+      onProgress({
+        phase: 'complete',
+        percent: 98,
+        message: 'Loading into KuzuDB...',
+        stats: {
+          filesProcessed: result.graph.nodeCount,
+          totalFiles: result.graph.nodeCount,
+          nodesCreated: result.graph.nodeCount,
+        },
+      });
+      
+      const kuzu = await getKuzuAdapter();
+      await kuzu.loadGraphToKuzu(result.graph, result.fileContents);
+      
+      if (import.meta.env.DEV) {
+        const stats = await kuzu.getKuzuStats();
+        console.log('KuzuDB loaded:', stats);
+        console.log('📁 Stored', storedFileContents.size, 'files for grep/read tools');
+      }
+    } catch {
+      // KuzuDB is optional - silently continue without it
+    }
+    
+    // Store clustering config for background enrichment (runs after graph loads)
+    if (clusteringConfig) {
+      pendingEnrichmentConfig = clusteringConfig;
+      console.log('📋 Clustering config saved for background enrichment');
+    }
+    
+    // Convert to serializable format for transfer back to main thread
+    return serializePipelineResult(result);
   },
 
   // ============================================================
@@ -341,8 +325,8 @@ const workerApi = {
     onProgress: (progress: EmbeddingProgress) => void,
     forceDevice?: 'webgpu' | 'wasm'
   ): Promise<void> {
-    const lbug = await getLbugAdapter();
-    if (!lbug.isLbugReady()) {
+    const kuzu = await getKuzuAdapter();
+    if (!kuzu.isKuzuReady()) {
       throw new Error('Database not ready. Please load a repository first.');
     }
 
@@ -359,8 +343,8 @@ const workerApi = {
     };
 
     await runEmbeddingPipeline(
-      lbug.executeQuery,
-      lbug.executeWithReusedStatement,
+      kuzu.executeQuery, 
+      kuzu.executeWithReusedStatement, 
       progressCallback,
       forceDevice ? { device: forceDevice } : {}
     );
@@ -416,15 +400,15 @@ const workerApi = {
     k: number = 10,
     maxDistance: number = 0.5
   ): Promise<SemanticSearchResult[]> {
-    const lbug = await getLbugAdapter();
-    if (!lbug.isLbugReady()) {
+    const kuzu = await getKuzuAdapter();
+    if (!kuzu.isKuzuReady()) {
       throw new Error('Database not ready. Please load a repository first.');
     }
     if (!isEmbeddingComplete) {
       throw new Error('Embeddings not ready. Please wait for embedding pipeline to complete.');
     }
 
-    return doSemanticSearch(lbug.executeQuery, query, k, maxDistance);
+    return doSemanticSearch(kuzu.executeQuery, query, k, maxDistance);
   },
 
   /**
@@ -440,15 +424,15 @@ const workerApi = {
     k: number = 5,
     hops: number = 2
   ): Promise<any[]> {
-    const lbug = await getLbugAdapter();
-    if (!lbug.isLbugReady()) {
+    const kuzu = await getKuzuAdapter();
+    if (!kuzu.isKuzuReady()) {
       throw new Error('Database not ready. Please load a repository first.');
     }
     if (!isEmbeddingComplete) {
       throw new Error('Embeddings not ready. Please wait for embedding pipeline to complete.');
     }
 
-    return doSemanticSearchWithContext(lbug.executeQuery, query, k, hops);
+    return doSemanticSearchWithContext(kuzu.executeQuery, query, k, hops);
   },
 
   /**
@@ -474,9 +458,9 @@ const workerApi = {
     let semanticResults: SemanticSearchResult[] = [];
     if (isEmbeddingComplete) {
       try {
-        const lbug = await getLbugAdapter();
-        if (lbug.isLbugReady()) {
-          semanticResults = await doSemanticSearch(lbug.executeQuery, query, k * 3, 0.5);
+        const kuzu = await getKuzuAdapter();
+        if (kuzu.isKuzuReady()) {
+          semanticResults = await doSemanticSearch(kuzu.executeQuery, query, k * 3, 0.5);
         }
       } catch {
         // Semantic search failed, continue with BM25 only
@@ -532,15 +516,15 @@ const workerApi = {
   },
 
   /**
-   * Test if LadybugDB supports array parameters in prepared statements
+   * Test if KuzuDB supports array parameters in prepared statements
    * This is a diagnostic function
    */
   async testArrayParams(): Promise<{ success: boolean; error?: string }> {
-    const lbug = await getLbugAdapter();
-    if (!lbug.isLbugReady()) {
+    const kuzu = await getKuzuAdapter();
+    if (!kuzu.isKuzuReady()) {
       return { success: false, error: 'Database not ready' };
     }
-    return lbug.testArrayParams();
+    return kuzu.testArrayParams();
   },
 
   // ============================================================
@@ -555,8 +539,8 @@ const workerApi = {
    */
   async initializeAgent(config: ProviderConfig, projectName?: string): Promise<{ success: boolean; error?: string }> {
     try {
-      const lbug = await getLbugAdapter();
-      if (!lbug.isLbugReady()) {
+      const kuzu = await getKuzuAdapter();
+      if (!kuzu.isKuzuReady()) {
         return { success: false, error: 'Database not ready. Please load a repository first.' };
       }
 
@@ -565,31 +549,31 @@ const workerApi = {
         if (!isEmbeddingComplete) {
           throw new Error('Embeddings not ready');
         }
-        return doSemanticSearch(lbug.executeQuery, query, k, maxDistance);
+        return doSemanticSearch(kuzu.executeQuery, query, k, maxDistance);
       };
 
       const semanticSearchWithContextWrapper = async (query: string, k?: number, hops?: number) => {
         if (!isEmbeddingComplete) {
           throw new Error('Embeddings not ready');
         }
-        return doSemanticSearchWithContext(lbug.executeQuery, query, k, hops);
+        return doSemanticSearchWithContext(kuzu.executeQuery, query, k, hops);
       };
 
       // Hybrid search wrapper - combines BM25 + semantic
       const hybridSearchWrapper = async (query: string, k?: number) => {
         // Get BM25 results (always available after ingestion)
         const bm25Results = searchBM25(query, (k ?? 10) * 3);
-
+        
         // Get semantic results if embeddings are ready
         let semanticResults: any[] = [];
         if (isEmbeddingComplete) {
           try {
-            semanticResults = await doSemanticSearch(lbug.executeQuery, query, (k ?? 10) * 3, 0.5);
+            semanticResults = await doSemanticSearch(kuzu.executeQuery, query, (k ?? 10) * 3, 0.5);
           } catch {
             // Semantic search failed, continue with BM25 only
           }
         }
-
+        
         // Merge with RRF
         return mergeWithRRF(bm25Results, semanticResults, k ?? 10);
       };
@@ -602,7 +586,7 @@ const workerApi = {
       
       let codebaseContext;
       try {
-        codebaseContext = await buildCodebaseContext(lbug.executeQuery, resolvedProjectName);
+        codebaseContext = await buildCodebaseContext(kuzu.executeQuery, resolvedProjectName);
         if (import.meta.env.DEV) {
           console.log('📊 Codebase context built:', {
             files: codebaseContext.stats.fileCount,
@@ -616,7 +600,7 @@ const workerApi = {
 
       currentAgent = createGraphRAGAgent(
         config,
-        lbug.executeQuery,
+        kuzu.executeQuery,
         semanticSearchWrapper,
         semanticSearchWithContextWrapper,
         hybridSearchWrapper,
@@ -643,7 +627,7 @@ const workerApi = {
 
   /**
    * Initialize the Graph RAG agent in backend mode (HTTP-backed tools).
-   * Uses HTTP wrappers instead of local LadybugDB for all tool queries.
+   * Uses HTTP wrappers instead of local KuzuDB for all tool queries.
    * @param config - Provider configuration for the LLM
    * @param backendUrl - Base URL of the gitnexus serve backend
    * @param repoName - Repository name on the backend
@@ -864,9 +848,9 @@ const workerApi = {
       }
     });
 
-    // Update LadybugDB with new data
+    // Update KuzuDB with new data
     try {
-      const lbug = await getLbugAdapter();
+      const kuzu = await getKuzuAdapter();
         
       onProgress(enrichments.size, enrichments.size); // Done
       
@@ -888,11 +872,11 @@ const workerApi = {
                c.enrichedBy = "llm"
          `;
          
-         await lbug.executeQuery(query);
+         await kuzu.executeQuery(query);
       }
-
+      
     } catch (err) {
-      console.error('Failed to update LadybugDB with enrichment:', err);
+      console.error('Failed to update KuzuDB with enrichment:', err);
     }
     
     // Convert Map to Record for serialization

gitnexus-web/src/workers/server-graph-hydration.test.ts

@@ -1,58 +0,0 @@
-import { describe, expect, it, vi } from 'vitest';
-
-import type { SerializablePipelineResult } from '../types/pipeline';
-import { buildPipelineResultFromSerialized, hydrateSerializedServerGraph } from './server-graph-hydration';
-
-describe('server graph hydration helpers', () => {
-  const serialized: SerializablePipelineResult = {
-    nodes: [
-      {
-        id: 'file:src/foo.ts',
-        label: 'File' as const,
-        properties: {
-          name: 'foo.ts',
-          filePath: 'src/foo.ts',
-          content: 'export function foo() {}',
-        },
-      },
-      {
-        id: 'func:src/foo.ts:foo',
-        label: 'Function' as const,
-        properties: {
-          name: 'foo',
-          filePath: 'src/foo.ts',
-        },
-      },
-    ],
-    relationships: [
-      {
-        source: 'file:src/foo.ts',
-        target: 'func:src/foo.ts:foo',
-        type: 'CONTAINS' as const,
-        properties: { type: 'CONTAINS' },
-      },
-    ],
-    fileContents: {
-      'src/foo.ts': 'export function foo() {}',
-    },
-  };
-
-  it('rebuilds a graph and file map from serialized server payloads', () => {
-    const result = buildPipelineResultFromSerialized(serialized);
-
-    expect(result.graph.nodeCount).toBe(2);
-    expect(result.graph.relationshipCount).toBe(1);
-    expect(result.fileContents.get('src/foo.ts')).toBe('export function foo() {}');
-  });
-
-  it('delegates the rebuilt result to the worker-side loader', async () => {
-    const loadResult = vi.fn().mockResolvedValue(undefined);
-
-    const result = await hydrateSerializedServerGraph(serialized, loadResult);
-
-    expect(loadResult).toHaveBeenCalledTimes(1);
-    expect(loadResult).toHaveBeenCalledWith(result);
-    expect(result.graph.nodeCount).toBe(2);
-    expect(result.fileContents.size).toBe(1);
-  });
-});

gitnexus-web/src/workers/server-graph-hydration.ts

@@ -1,24 +0,0 @@
-import { createKnowledgeGraph } from '../core/graph/graph';
-import type { PipelineResult, SerializablePipelineResult } from '../types/pipeline';
-
-export const buildPipelineResultFromSerialized = (
-  serialized: SerializablePipelineResult,
-): PipelineResult => {
-  const graph = createKnowledgeGraph();
-  serialized.nodes.forEach((node) => graph.addNode(node));
-  serialized.relationships.forEach((relationship) => graph.addRelationship(relationship));
-
-  return {
-    graph,
-    fileContents: new Map(Object.entries(serialized.fileContents)),
-  };
-};
-
-export const hydrateSerializedServerGraph = async (
-  serialized: SerializablePipelineResult,
-  loadResult: (result: PipelineResult) => Promise<void>,
-): Promise<PipelineResult> => {
-  const result = buildPipelineResultFromSerialized(serialized);
-  await loadResult(result);
-  return result;
-};

gitnexus-web/test/setup.ts

@@ -1,6 +0,0 @@
-import { beforeEach } from 'vitest';
-
-beforeEach(() => {
-  sessionStorage.clear();
-  localStorage.clear();
-});

gitnexus-web/test/unit/bug-fixes.test.ts

@@ -1,259 +0,0 @@
-import { describe, expect, it } from 'vitest';
-import { createKnowledgeGraph } from '../../src/core/graph/graph';
-
-// ==========================================================================
-// PR1 Bug Fix Tests — positive and negative cases
-// Tests the data structures and logic underlying the 4 bug fixes without
-// requiring WASM (LadybugDB is skipped in test env via isTestEnv()).
-// ==========================================================================
-
-describe('createKnowledgeGraph — data integrity for loadServerGraph', () => {
-  // Positive: nodes and relationships are stored correctly
-  it('stores nodes added via addNode', () => {
-    const graph = createKnowledgeGraph();
-    graph.addNode({
-      id: 'Function:src/index.ts:main',
-      label: 'Function',
-      properties: { name: 'main', filePath: 'src/index.ts', startLine: 1, endLine: 10 },
-    });
-
-    expect(graph.nodes).toHaveLength(1);
-    expect(graph.nodes[0].id).toBe('Function:src/index.ts:main');
-    expect(graph.nodes[0].label).toBe('Function');
-    expect(graph.nodes[0].properties.name).toBe('main');
-  });
-
-  it('stores relationships added via addRelationship', () => {
-    const graph = createKnowledgeGraph();
-    graph.addNode({
-      id: 'Function:a.ts:foo',
-      label: 'Function',
-      properties: { name: 'foo', filePath: 'a.ts', startLine: 1, endLine: 5 },
-    });
-    graph.addNode({
-      id: 'Function:a.ts:bar',
-      label: 'Function',
-      properties: { name: 'bar', filePath: 'a.ts', startLine: 10, endLine: 15 },
-    });
-    graph.addRelationship({
-      sourceId: 'Function:a.ts:foo',
-      targetId: 'Function:a.ts:bar',
-      type: 'CALLS',
-      properties: {},
-    });
-
-    expect(graph.relationships).toHaveLength(1);
-    expect(graph.relationships[0].type).toBe('CALLS');
-    expect(graph.relationships[0].sourceId).toBe('Function:a.ts:foo');
-    expect(graph.relationships[0].targetId).toBe('Function:a.ts:bar');
-  });
-
-  // Positive: deduplication works
-  it('deduplicates nodes with the same id', () => {
-    const graph = createKnowledgeGraph();
-    graph.addNode({
-      id: 'File:src/index.ts',
-      label: 'File',
-      properties: { name: 'index.ts', filePath: 'src/index.ts' },
-    });
-    graph.addNode({
-      id: 'File:src/index.ts',
-      label: 'File',
-      properties: { name: 'index.ts', filePath: 'src/index.ts' },
-    });
-
-    expect(graph.nodes).toHaveLength(1);
-  });
-
-  // Positive: nodeCount reflects actual count
-  it('nodeCount matches number of unique nodes', () => {
-    const graph = createKnowledgeGraph();
-    graph.addNode({
-      id: 'File:a.ts',
-      label: 'File',
-      properties: { name: 'a.ts', filePath: 'a.ts' },
-    });
-    graph.addNode({
-      id: 'File:b.ts',
-      label: 'File',
-      properties: { name: 'b.ts', filePath: 'b.ts' },
-    });
-
-    expect(graph.nodeCount).toBe(2);
-  });
-
-  // Negative: empty graph has zero counts
-  it('empty graph has zero nodes and relationships', () => {
-    const graph = createKnowledgeGraph();
-    expect(graph.nodes).toHaveLength(0);
-    expect(graph.relationships).toHaveLength(0);
-    expect(graph.nodeCount).toBe(0);
-  });
-
-  // Negative: relationships with missing source/target still stored
-  // (validation is upstream, graph is a dumb container)
-  it('stores relationships even with non-existent node IDs', () => {
-    const graph = createKnowledgeGraph();
-    graph.addRelationship({
-      sourceId: 'NonExistent:a',
-      targetId: 'NonExistent:b',
-      type: 'CALLS',
-      properties: {},
-    });
-
-    expect(graph.relationships).toHaveLength(1);
-  });
-});
-
-describe('loadServerGraph — data flow validation', () => {
-  // Positive: server data can be reconstructed into a KnowledgeGraph
-  it('reconstructs graph from server node/relationship arrays', () => {
-    const graph = createKnowledgeGraph();
-    const serverNodes = [
-      { id: 'File:src/app.ts', label: 'File' as const, properties: { name: 'app.ts', filePath: 'src/app.ts' } },
-      { id: 'Function:src/app.ts:main', label: 'Function' as const, properties: { name: 'main', filePath: 'src/app.ts', startLine: 1, endLine: 20 } },
-    ];
-    const serverRels = [
-      { sourceId: 'File:src/app.ts', targetId: 'Function:src/app.ts:main', type: 'CONTAINS' as const, properties: {} },
-    ];
-
-    for (const node of serverNodes) graph.addNode(node);
-    for (const rel of serverRels) graph.addRelationship(rel);
-
-    expect(graph.nodeCount).toBe(2);
-    expect(graph.relationships).toHaveLength(1);
-    expect(graph.relationships[0].type).toBe('CONTAINS');
-  });
-
-  // Positive: file contents map is built correctly from server data
-  it('builds fileContents Map from server object entries', () => {
-    const serverFileContents: Record<string, string> = {
-      'src/index.ts': 'export function main() {}',
-      'src/utils.ts': 'export const helper = () => {}',
-    };
-
-    const fileMap = new Map<string, string>();
-    for (const [path, content] of Object.entries(serverFileContents)) {
-      fileMap.set(path, content);
-    }
-
-    expect(fileMap.size).toBe(2);
-    expect(fileMap.get('src/index.ts')).toBe('export function main() {}');
-    expect(fileMap.get('src/utils.ts')).toContain('helper');
-  });
-
-  // Negative: empty server response produces empty graph
-  it('handles empty server data gracefully', () => {
-    const graph = createKnowledgeGraph();
-    const serverNodes: any[] = [];
-    const serverRels: any[] = [];
-
-    for (const node of serverNodes) graph.addNode(node);
-    for (const rel of serverRels) graph.addRelationship(rel);
-
-    expect(graph.nodeCount).toBe(0);
-    expect(graph.relationships).toHaveLength(0);
-  });
-
-  // Negative: fileContents replaces (not accumulates) on reload
-  it('fileContents map replacement prevents stale data', () => {
-    // Simulates the storedFileContents = fileMap assignment in loadServerGraph
-    let storedFileContents = new Map<string, string>();
-    storedFileContents.set('old-file.ts', 'old content');
-
-    // Second load replaces the map entirely
-    const newFileMap = new Map<string, string>();
-    newFileMap.set('new-file.ts', 'new content');
-    storedFileContents = newFileMap; // assignment, not merge
-
-    expect(storedFileContents.size).toBe(1);
-    expect(storedFileContents.has('old-file.ts')).toBe(false);
-    expect(storedFileContents.get('new-file.ts')).toBe('new content');
-  });
-});
-
-describe('BM25 index — argument type validation', () => {
-  // Positive: Map<string, string> has the expected interface for BM25
-  it('Map has entries() and size for BM25 indexing', () => {
-    const fileMap = new Map<string, string>([
-      ['src/a.ts', 'function foo() {}'],
-      ['src/b.ts', 'function bar() {}'],
-    ]);
-
-    expect(fileMap.size).toBe(2);
-    expect(typeof fileMap.entries).toBe('function');
-
-    // Verify iteration works (BM25 iterates entries)
-    const entries = Array.from(fileMap.entries());
-    expect(entries).toHaveLength(2);
-    expect(entries[0][0]).toBe('src/a.ts');
-  });
-
-  // Negative: a KnowledgeGraph object does NOT have entries()
-  // This was the original bug — passing graph instead of fileMap
-  it('KnowledgeGraph does not have entries() (the original bug)', () => {
-    const graph = createKnowledgeGraph();
-    expect((graph as any).entries).toBeUndefined();
-  });
-});
-
-describe('highlight clearing — state management', () => {
-  // Positive: Set operations for highlight clearing
-  it('clearing a Set produces an empty set', () => {
-    const highlights = new Set(['node1', 'node2', 'node3']);
-    const cleared = new Set<string>();
-
-    expect(cleared.size).toBe(0);
-    expect(highlights.size).toBe(3);
-  });
-
-  // Positive: multiple highlight sources are independent
-  it('independent highlight sets can be cleared separately', () => {
-    const processHighlights = new Set(['proc_1', 'proc_2']);
-    const aiToolHighlights = new Set(['Function:a.ts:foo']);
-    const aiCitationHighlights = new Set(['File:b.ts']);
-    const blastRadius = new Set(['Function:c.ts:bar']);
-
-    // Simulate "Turn off all highlights" — clear all sets
-    const clearedProcess = new Set<string>();
-    const clearedAITool = new Set<string>();
-    const clearedAICitation = new Set<string>();
-    const clearedBlast = new Set<string>();
-
-    expect(clearedProcess.size).toBe(0);
-    expect(clearedAITool.size).toBe(0);
-    expect(clearedAICitation.size).toBe(0);
-    expect(clearedBlast.size).toBe(0);
-
-    // Original sets unchanged (React state immutability)
-    expect(processHighlights.size).toBe(2);
-    expect(aiToolHighlights.size).toBe(1);
-  });
-
-  // Negative: clearing highlights doesn't affect node selection
-  // (selection is a separate state — verified by checking they're independent)
-  it('highlight state is independent from node selection state', () => {
-    const highlights = new Set(['node1']);
-    let selectedNode: { id: string } | null = { id: 'node1' };
-
-    // Clear highlights but keep selection
-    const clearedHighlights = new Set<string>();
-    expect(clearedHighlights.size).toBe(0);
-    expect(selectedNode).not.toBeNull();
-
-    // Clear selection independently
-    selectedNode = null;
-    expect(selectedNode).toBeNull();
-  });
-
-  // Negative: toggling AI highlights ON should NOT clear user query highlights
-  it('AI highlight toggle does not clear process highlights', () => {
-    const processHighlights = new Set(['proc_1', 'proc_2']);
-    let isAIEnabled = false;
-
-    // Turn AI on — process highlights should survive
-    isAIEnabled = true;
-    expect(processHighlights.size).toBe(2);
-    expect(isAIEnabled).toBe(true);
-  });
-});

gitnexus-web/tsconfig.app.json

@@ -20,6 +20,5 @@
     },
     "types": ["vite/client"]
   },
-  "include": ["src"],
-  "exclude": ["src/**/*.test.ts", "src/**/*.test.tsx"]
+  "include": ["src"]
 }

gitnexus-web/vite.config.ts

@@ -12,11 +12,11 @@ export default defineConfig({
     tailwindcss(),
     wasm(),
     topLevelAwait(),
-    // Copy lbug-wasm worker file to assets folder for production
+    // Copy kuzu-wasm worker file to assets folder for production
     viteStaticCopy({
       targets: [
         {
-          src: 'node_modules/@ladybugdb/wasm-core/lbug_wasm_worker.js',
+          src: 'node_modules/kuzu-wasm/kuzu_wasm_worker.js',
           dest: 'assets'
         }
       ]
@@ -35,12 +35,12 @@ export default defineConfig({
   define: {
     global: 'globalThis',
   },
-  // Optimize deps - exclude lbug-wasm from pre-bundling (it has WASM files)
+  // Optimize deps - exclude kuzu-wasm from pre-bundling (it has WASM files)
   optimizeDeps: {
-    exclude: ['@ladybugdb/wasm-core'],
+    exclude: ['kuzu-wasm'],
     include: ['buffer'],
   },
-  // Required for LadybugDB WASM (SharedArrayBuffer needs Cross-Origin Isolation)
+  // Required for KuzuDB WASM (SharedArrayBuffer needs Cross-Origin Isolation)
   server: {
     headers: {
       'Cross-Origin-Opener-Policy': 'same-origin',

gitnexus-web/vitest.config.ts

@@ -1,17 +0,0 @@
-import { defineConfig } from 'vitest/config';
-import path from 'path';
-
-export default defineConfig({
-  test: {
-    environment: 'jsdom',
-    globals: true,
-    setupFiles: ['test/setup.ts'],
-    include: ['test/**/*.test.ts'],
-    exclude: ['**/node_modules/**', '**/dist/**'],
-  },
-  resolve: {
-    alias: {
-      '@': path.resolve(__dirname, './src'),
-    },
-  },
-});

gitnexus/.claude/settings.local.json

@@ -1,7 +0,0 @@
-{
-  "permissions": {
-    "allow": [
-      "mcp__plugin_claude-mem_mcp-search__get_observations"
-    ]
-  }
-}

gitnexus/.env.example

@@ -1,12 +0,0 @@
-# GitNexus HTTP Embedding Configuration
-# Copy to .env and uncomment to use a remote OpenAI-compatible endpoint
-# instead of the local snowflake-arctic-embed-xs model.
-# When unset, local embeddings are used unchanged.
-
-# GITNEXUS_EMBEDDING_URL=http://your-server:8080/v1
-# GITNEXUS_EMBEDDING_MODEL=BAAI/bge-large-en-v1.5
-# GITNEXUS_EMBEDDING_DIMS=1024
-# GITNEXUS_EMBEDDING_API_KEY=your-key
-
-# Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI.
-# See README for details.

gitnexus/CHANGELOG.md

@@ -1,159 +0,0 @@
-# Changelog
-
-All notable changes to GitNexus will be documented in this file.
-
-## [1.4.8] - 2026-03-23
-
-### Added
-- **Type resolution Milestone D — Phases 10–13** consolidated into a single milestone with full integration test coverage across 11 languages (#387)
-  - Phase A/B/C: overload disambiguation via argument literal types, constructor-visible virtual dispatch via `constructorTypeMap`, `parameterTypes` extraction in `extractMethodSignature`
-  - Phase 14 enhancements: single-pass seeding, Tarjan's SCC for cyclic resolution, cross-file return types
-  - Optional parameter arity resolution
-  - Per-language cross-file binding tests and resolver fixes
-  - Store all overloads in `fileIndex` instead of last-write-wins
-- **Cross-file binding propagation** for multiple languages
-- **HTTP embedding backend** for self-hosted/remote endpoints with dynamic dimensions, batch guards, and dimension mismatch handling (#395)
-- **Markdown file indexing** — headings and cross-links as graph nodes (#399)
-- **MiniMax provider support** (#224)
-- **Codex MCP and skills support** with CLI setup flow and e2e tests
-- **HelpPanel UI** — built-in help for the web interface (#465)
-- **Section node type** registered in `NODE_TABLES` and `NODE_SCHEMA_QUERIES` (#401)
-- **Community and Process node properties** documented in cypher tool description (#411)
-- **Server-mode hydration regression tests**
-- **Pre-commit hooks** via husky for typecheck + unit tests
-
-### Fixed
-- **Python import alias resolution** — `import X as Y` now routes module aliases directly to `moduleAliasMap` in import processor (#417, #461)
-- **Python module-qualified calls** resolved via `moduleAliasMap` (#337)
-- **Python module-qualified constructor calls** (Issue #337)
-- **Heritage/MRO edges** now calculate confidence per resolution tier (#412)
-- **LadybugDB lock** — retry on DB lock with session-safe cleanup (#325)
-- **CORS** — allow private/LAN network origins (#390)
-- **Analyze without git** — allow indexing folders without a `.git` directory (#384)
-- **Web: LadybugDB** — `getAllRows`, `loadServerGraph`, BM25, highlight clearing (#474)
-- **Server-mode hydration** — await server connect hydration flow (#398, #404)
-- **Embedding dimensions** — validate on every vector, not just the first; hard-throw on mismatch
-- **Timeout detection** — always-on dim validation, test hardening
-- **ONNX CUDA** — prevent uncatchable native crash when CUDA libs present but ORT lacks CUDA provider; clarify linux/x64-only
-- **CLI** — run codex mcp add via shell on Windows; write tool output to stdout via fd 1
-- **Stale progress, cross-platform prepare, DEV log** fixes
-- **Import resolution API** simplified per PR #409 review findings (P0–P3)
-- **Auto-labeling** — switched from clustering to z-score method; multi-dim aware Mahalanobis threshold
-- **PR/issue filtering** — fixed prop cutoff issue
-- **Sequential enrichment queries** + stale data detection
-- **package-lock.json** synced with `onnxruntime-node ^1.24.0`
-
-### Changed
-- **Unified language dispatch** with compile-time exhaustive tables
-- **Prepare script simplified** — removed `scripts/prepare.cjs`
-- **Switched from .githooks to husky** for pre-commit hooks
-- **`@claude` workflow** restricted to maintainers and above via `author_association` check
-
-### Performance
-- **O(1) per-chunk synthesis guard** using `boolean[]` instead of Set
-- **`sizeBefore` optimization** in type resolution
-- **Token truncation** improvements
-
-### Chore
-- Strengthened Python module-import tests, un-skipped match/case, added perf guard
-- Added positive and negative tests for all 4 bug fixes
-- E2e tests for stale detection, sequential enrichment, stability (#396)
-- Integration tests for Milestone D across all 11 languages
-- `gitnexus-stable-ops` added to community integrations
-- `.env.example` added for embedding backend configuration
-
-## [1.4.7] - 2026-03-19
-
-### Added
-- **Phase 8 field/property type resolution** — ACCESSES edges with `declaredType` for field reads/writes (#354)
-- **Phase 9 return-type variable binding** — call-result variable binding across 11 languages (#379)
-  - `extractPendingAssignment` in per-language type extractors captures `let x = getUser()` patterns
-  - Unified fixpoint loop resolves variable types from function return types after initial walk
-  - Field access on call-result variables: `user.name` resolves `name` via return type's class definition
-  - Method-call-result chaining: `user.getProfile().bio` resolves through intermediate return types
-  - 22 new test fixtures covering call-result and method-chain binding across all supported languages
-  - Integration tests added for all 10 language resolver suites
-- **ACCESSES edge type** with read/write field access tracking (#372)
-- **Python `enumerate()` for-loop support** with nested tuple patterns (#356)
-- **MCP tool/resource descriptions** updated to reflect Phase 9 ACCESSES edge semantics and `declaredType` property
-
-### Fixed
-- **mcp**: server crashes under parallel tool calls (#326, #349)
-- **parsing**: undefined error on languages missing from call routers (#364)
-- **web**: add missing Kotlin entries to `Record<SupportedLanguages>` maps
-- **rust**: `await` expression unwrapping in `extractPendingAssignment` for async call-result binding
-- **tests**: update property edge and write access expectations across multiple language tests
-- **docs**: corrected stale "single-pass" claims in type-resolution-system.md to reflect walk+fixpoint architecture
-
-### Changed
-- **Upgrade `@ladybugdb/core` to 0.15.2** and remove segfault workarounds (#374)
-- **type-resolution-roadmap.md** overhauled — completed phases condensed to summaries, Phases 10–14 added with full engineering specs
-
-## [1.4.6] - 2026-03-18
-
-### Added
-- **Phase 7 type resolution** — return-aware loop inference for call-expression iterables (#341)
-  - `ReturnTypeLookup` interface with `lookupReturnType` / `lookupRawReturnType` split
-  - `ForLoopExtractorContext` context object replacing positional `(node, env)` signature
-  - Call-expression iterable resolution across 8 languages (TS/JS, Java, Kotlin, C#, Go, Rust, Python, PHP)
-  - PHP `$this->property` foreach via `@var` class property scan (Strategy C)
-  - PHP `function_call_expression` and `member_call_expression` foreach paths
-  - `extractElementTypeFromString` as canonical raw-string container unwrapper in `shared.ts`
-  - `extractReturnTypeName` deduplicated from `call-processor.ts` into `shared.ts` (137 lines removed)
-  - `SKIP_SUBTREE_TYPES` performance optimization with documented `template_string` exclusion
-  - `pendingCallResults` infrastructure (dormant — Phase 9 work)
-
-### Fixed
-- **impact**: return structured error + partial results instead of crashing (#345)
-- **impact**: add `HAS_METHOD` and `OVERRIDES` to `VALID_RELATION_TYPES` (#350)
-- **cli**: write tool output to stdout via fd 1 instead of stderr (#346)
-- **postinstall**: add permission fix for CLI and hook scripts (#348)
-- **workflow**: use prefixed temporary branch name for fork PRs to prevent overwriting real branches
-- **test**: add `--repo` to CLI e2e tool tests for multi-repo environment
-- **php**: add `declaration_list` type guard on `findClassPropertyElementType` fallback
-- **docs**: correct `pendingCallResults` description in roadmap and system docs
-
-### Chore
-- Add `.worktrees/` to `.gitignore`
-
-## [1.4.5] - 2026-03-17
-
-### Added
-- **Ruby language support** for CLI and web (#111)
-- **TypeEnvironment API** with constructor inference, self/this/super resolution (#274)
-- **Return type inference** with doc-comment parsing (JSDoc, PHPDoc, YARD) and per-language type extractors (#284)
-- **Phase 4 type resolution** — nullable unwrapping, for-loop typing, assignment chain propagation (#310)
-- **Phase 5 type resolution** — chained calls, pattern matching, class-as-receiver (#315)
-- **Phase 6 type resolution** — for-loop Tier 1c, pattern matching, container descriptors, 10-language coverage (#318)
-  - Container descriptor table for generic type argument resolution (Map keys vs values)
-  - Method-aware for-loop extractors with integration tests for all languages
-  - Recursive pattern binding (C# `is` patterns, Kotlin `when/is` smart casts)
-  - Class field declaration unwrapping for C#/Java
-  - PHP `$this->property` foreach member access
-  - C++ pointer dereference range-for
-  - Java `this.data.values()` field access patterns
-  - Position-indexed when/is bindings for branch-local narrowing
-- **Type resolution system documentation** with architecture guide and roadmap
-- `.gitignore` and `.gitnexusignore` support during file discovery (#231)
-- Codex MCP configuration documentation in README (#236)
-- `skipGraphPhases` pipeline option to skip MRO/community/process phases for faster test runs
-- `hookTimeout: 120000` in vitest config for CI beforeAll hooks
-
-### Changed
-- **Migrated from KuzuDB to LadybugDB v0.15** (#275)
-- Dynamically discover and install agent skills in CLI (#270)
-
-### Performance
-- Worker pool threshold — skip worker creation for small repos (<15 files or <512KB total)
-- AST walk pruning via `SKIP_SUBTREE_TYPES` for leaf-only nodes (string, comment, number literals)
-- Pre-computed `interestingNodeTypes` set — single Set.has() replaces 3 checks per AST node
-- `fastStripNullable` — skip full nullable parsing for simple identifiers (90%+ case)
-- Replace `.children?.find()` with manual for loops in `extractFunctionName` to eliminate array allocations
-
-### Fixed
-- Same-directory Python import resolution (#328)
-- Ruby method-level call resolution, HAS_METHOD edges, and dispatch table (#278)
-- C++ fixture file casing for case-sensitive CI
-- Template string incorrectly included in AST pruning set (contains interpolated expressions)
-
-## [1.4.0] - Previous release

gitnexus/Dockerfile.test

@@ -1,9 +0,0 @@
-FROM node:22-bookworm
-WORKDIR /app
-RUN apt-get update && apt-get install -y python3 make g++ && rm -rf /var/lib/apt/lists/*
-COPY . .
-RUN npm ci --ignore-scripts \
-    && node scripts/patch-tree-sitter-swift.cjs \
-    && (npm rebuild 2>&1 || true) \
-    && cd node_modules/tree-sitter-kotlin && npx --yes node-gyp rebuild 2>&1
-CMD ["npx", "vitest", "run", "test/integration", "--reporter=verbose"]

gitnexus/README.md

@@ -2,7 +2,7 @@
 
 **Graph-powered code intelligence for AI agents.** Index any codebase into a knowledge graph, then query it via MCP or CLI.
 
-Works with **Cursor**, **Claude Code**, **Codex**, **Windsurf**, **Cline**, **OpenCode**, and any MCP-compatible tool.
+Works with **Cursor**, **Claude Code**, **Windsurf**, **Cline**, **OpenCode**, and any MCP-compatible tool.
 
 [![npm version](https://img.shields.io/npm/v/gitnexus.svg)](https://www.npmjs.com/package/gitnexus)
 [![License: PolyForm Noncommercial](https://img.shields.io/badge/License-PolyForm%20Noncommercial-blue.svg)](https://polyformproject.org/licenses/noncommercial/1.0.0/)
@@ -34,7 +34,6 @@ To configure MCP for your editor, run `npx gitnexus setup` once — or set it up
 |--------|-----|--------|---------------------|---------|
 | **Claude Code** | Yes | Yes | Yes (PreToolUse) | **Full** |
 | **Cursor** | Yes | Yes | — | MCP + Skills |
-| **Codex** | Yes | Yes | — | MCP + Skills |
 | **Windsurf** | Yes | — | — | MCP |
 | **OpenCode** | Yes | Yes | — | MCP + Skills |
 
@@ -56,12 +55,6 @@ If you prefer to configure manually instead of using `gitnexus setup`:
 claude mcp add gitnexus -- npx -y gitnexus@latest mcp
 ```
 
-### Codex (full support — MCP + skills)
-
-```bash
-codex mcp add gitnexus -- npx -y gitnexus@latest mcp
-```
-
 ### Cursor / Windsurf
 
 Add to `~/.cursor/mcp.json` (global — works for all projects):
@@ -103,7 +96,7 @@ GitNexus builds a complete knowledge graph of your codebase through a multi-phas
 5. **Processes** — Traces execution flows from entry points through call chains
 6. **Search** — Builds hybrid search indexes for fast retrieval
 
-The result is a **LadybugDB graph database** stored locally in `.gitnexus/` with full-text search and semantic embeddings.
+The result is a **KuzuDB graph database** stored locally in `.gitnexus/` with full-text search and semantic embeddings.
 
 ## MCP Tools
 
@@ -146,8 +139,7 @@ Your AI agent gets these tools automatically:
 gitnexus setup                    # Configure MCP for your editors (one-time)
 gitnexus analyze [path]           # Index a repository (or update stale index)
 gitnexus analyze --force          # Force full re-index
-gitnexus analyze --embeddings     # Enable embedding generation (slower, better search)
-gitnexus analyze --verbose        # Log skipped files when parsers are unavailable
+gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
 gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
 gitnexus serve                   # Start local HTTP server (multi-repo) for web UI
 gitnexus list                    # List all indexed repositories
@@ -158,47 +150,13 @@ gitnexus wiki [path]             # Generate LLM-powered docs from knowledge grap
 gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
 ```
 
-## Remote Embeddings
-
-Set these env vars to use a remote OpenAI-compatible `/v1/embeddings` endpoint instead of the local model:
-
-```bash
-export GITNEXUS_EMBEDDING_URL=http://your-server:8080/v1
-export GITNEXUS_EMBEDDING_MODEL=BAAI/bge-large-en-v1.5
-export GITNEXUS_EMBEDDING_DIMS=1024          # optional, default 384
-export GITNEXUS_EMBEDDING_API_KEY=your-key   # optional, default: "unused"
-gitnexus analyze . --embeddings
-```
-
-Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. When unset, local embeddings are used unchanged.
-
 ## Multi-Repo Support
 
 GitNexus supports indexing multiple repositories. Each `gitnexus analyze` registers the repo in a global registry (`~/.gitnexus/registry.json`). The MCP server serves all indexed repos automatically.
 
 ## Supported Languages
 
-TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Kotlin, Swift, Ruby
-
-### Language Feature Matrix
-
-| Language | Imports | Named Bindings | Exports | Heritage | Type Annotations | Constructor Inference | Config | Frameworks | Entry Points |
-|----------|---------|----------------|---------|----------|-----------------|---------------------|--------|------------|-------------|
-| TypeScript | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| JavaScript | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ |
-| Python | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Java | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| Kotlin | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| C# | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Go | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Rust | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-| PHP | ✓ | ✓ | ✓ | — | ✓ | ✓ | ✓ | ✓ | ✓ |
-| Ruby | ✓ | — | ✓ | ✓ | — | ✓ | — | ✓ | ✓ |
-| Swift | — | — | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
-| C | — | — | ✓ | — | ✓ | ✓ | — | ✓ | ✓ |
-| C++ | — | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
-
-**Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics
+TypeScript, JavaScript, Python, Java, C, C++, C#, Go, Rust, PHP, Swift
 
 ## Agent Skills
 

gitnexus/hooks/claude/gitnexus-hook.cjs

@@ -2,10 +2,8 @@
 /**
  * GitNexus Claude Code Hook
  *
- * PreToolUse  — intercepts Grep/Glob/Bash searches and augments
- *               with graph context from the GitNexus index.
- * PostToolUse — detects stale index after git mutations and notifies
- *               the agent to reindex.
+ * PreToolUse handler — intercepts Grep/Glob/Bash searches
+ * and augments with graph context from the GitNexus index.
  *
  * NOTE: SessionStart hooks are broken on Windows (Claude Code bug).
  * Session context is injected via CLAUDE.md / skills instead.
@@ -13,7 +11,7 @@
 
 const fs = require('fs');
 const path = require('path');
-const { spawnSync } = require('child_process');
+const { execFileSync } = require('child_process');
 
 /**
  * Read JSON input from stdin synchronously.
@@ -28,19 +26,19 @@ function readInput() {
 }
 
 /**
- * Find the .gitnexus directory by walking up from startDir.
- * Returns the path to .gitnexus/ or null if not found.
+ * Check if a directory (or ancestor) has a .gitnexus index.
  */
-function findGitNexusDir(startDir) {
+function findGitNexusIndex(startDir) {
   let dir = startDir || process.cwd();
   for (let i = 0; i < 5; i++) {
-    const candidate = path.join(dir, '.gitnexus');
-    if (fs.existsSync(candidate)) return candidate;
+    if (fs.existsSync(path.join(dir, '.gitnexus'))) {
+      return true;
+    }
     const parent = path.dirname(dir);
     if (parent === dir) break;
     dir = parent;
   }
-  return null;
+  return false;
 }
 
 /**
@@ -85,153 +83,72 @@ function extractPattern(toolName, toolInput) {
   return null;
 }
 
-/**
- * Resolve the gitnexus CLI path.
- * 1. Relative path (works when script is inside npm package)
- * 2. require.resolve (works when gitnexus is globally installed)
- * 3. Fall back to npx (returns empty string)
- */
-function resolveCliPath() {
-  let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');
-  if (!fs.existsSync(cliPath)) {
-    try {
-      cliPath = require.resolve('gitnexus/dist/cli/index.js');
-    } catch {
-      cliPath = '';
-    }
-  }
-  return cliPath;
-}
-
-/**
- * Spawn a gitnexus CLI command synchronously.
- * Returns the stderr output (KuzuDB captures stdout at OS level).
- */
-function runGitNexusCli(cliPath, args, cwd, timeout) {
-  const isWin = process.platform === 'win32';
-  if (cliPath) {
-    return spawnSync(
-      process.execPath,
-      [cliPath, ...args],
-      { encoding: 'utf-8', timeout, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
-    );
-  }
-  // On Windows, invoke npx.cmd directly (no shell needed)
-  return spawnSync(
-    isWin ? 'npx.cmd' : 'npx',
-    ['-y', 'gitnexus', ...args],
-    { encoding: 'utf-8', timeout: timeout + 5000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
-  );
-}
-
-/**
- * PreToolUse handler — augment searches with graph context.
- */
-function handlePreToolUse(input) {
-  const cwd = input.cwd || process.cwd();
-  if (!path.isAbsolute(cwd)) return;
-  if (!findGitNexusDir(cwd)) return;
-
-  const toolName = input.tool_name || '';
-  const toolInput = input.tool_input || {};
-
-  if (toolName !== 'Grep' && toolName !== 'Glob' && toolName !== 'Bash') return;
-
-  const pattern = extractPattern(toolName, toolInput);
-  if (!pattern || pattern.length < 3) return;
-
-  const cliPath = resolveCliPath();
-  let result = '';
-  try {
-    const child = runGitNexusCli(cliPath, ['augment', '--', pattern], cwd, 7000);
-    if (!child.error && child.status === 0) {
-      result = child.stderr || '';
-    }
-  } catch { /* graceful failure */ }
-
-  if (result && result.trim()) {
-    sendHookResponse('PreToolUse', result.trim());
-  }
-}
-
-/**
- * Emit a PostToolUse hook response with additional context for the agent.
- */
-function sendHookResponse(hookEventName, message) {
-  console.log(JSON.stringify({
-    hookSpecificOutput: { hookEventName, additionalContext: message }
-  }));
-}
-
-/**
- * PostToolUse handler — detect index staleness after git mutations.
- *
- * Instead of spawning a full `gitnexus analyze` synchronously (which blocks
- * the agent for up to 120s and risks KuzuDB corruption on timeout), we do a
- * lightweight staleness check: compare `git rev-parse HEAD` against the
- * lastCommit stored in `.gitnexus/meta.json`. If they differ, notify the
- * agent so it can decide when to reindex.
- */
-function handlePostToolUse(input) {
-  const toolName = input.tool_name || '';
-  if (toolName !== 'Bash') return;
-
-  const command = (input.tool_input || {}).command || '';
-  if (!/\bgit\s+(commit|merge|rebase|cherry-pick|pull)(\s|$)/.test(command)) return;
-
-  // Only proceed if the command succeeded
-  const toolOutput = input.tool_output || {};
-  if (toolOutput.exit_code !== undefined && toolOutput.exit_code !== 0) return;
-
-  const cwd = input.cwd || process.cwd();
-  if (!path.isAbsolute(cwd)) return;
-  const gitNexusDir = findGitNexusDir(cwd);
-  if (!gitNexusDir) return;
-
-  // Compare HEAD against last indexed commit — skip if unchanged
-  let currentHead = '';
-  try {
-    const headResult = spawnSync('git', ['rev-parse', 'HEAD'], {
-      encoding: 'utf-8', timeout: 3000, cwd, stdio: ['pipe', 'pipe', 'pipe'],
-    });
-    currentHead = (headResult.stdout || '').trim();
-  } catch { return; }
-
-  if (!currentHead) return;
-
-  let lastCommit = '';
-  let hadEmbeddings = false;
-  try {
-    const meta = JSON.parse(fs.readFileSync(path.join(gitNexusDir, 'meta.json'), 'utf-8'));
-    lastCommit = meta.lastCommit || '';
-    hadEmbeddings = (meta.stats && meta.stats.embeddings > 0);
-  } catch { /* no meta — treat as stale */ }
-
-  // If HEAD matches last indexed commit, no reindex needed
-  if (currentHead && currentHead === lastCommit) return;
-
-  const analyzeCmd = `npx gitnexus analyze${hadEmbeddings ? ' --embeddings' : ''}`;
-  sendHookResponse('PostToolUse',
-    `GitNexus index is stale (last indexed: ${lastCommit ? lastCommit.slice(0, 7) : 'never'}). ` +
-    `Run \`${analyzeCmd}\` to update the knowledge graph.`
-  );
-}
-
-// Dispatch map for hook events
-const handlers = {
-  PreToolUse: handlePreToolUse,
-  PostToolUse: handlePostToolUse,
-};
-
 function main() {
   try {
     const input = readInput();
-    const handler = handlers[input.hook_event_name || ''];
-    if (handler) handler(input);
-  } catch (err) {
-    if (process.env.GITNEXUS_DEBUG) {
-      console.error('GitNexus hook error:', (err.message || '').slice(0, 200));
+    const hookEvent = input.hook_event_name || '';
+
+    if (hookEvent !== 'PreToolUse') return;
+
+    const cwd = input.cwd || process.cwd();
+    if (!findGitNexusIndex(cwd)) return;
+
+    const toolName = input.tool_name || '';
+    const toolInput = input.tool_input || {};
+
+    if (toolName !== 'Grep' && toolName !== 'Glob' && toolName !== 'Bash') return;
+
+    const pattern = extractPattern(toolName, toolInput);
+    if (!pattern || pattern.length < 3) return;
+
+    // Resolve CLI path — try multiple strategies:
+    // 1. Relative path (works when script is inside npm package)
+    // 2. require.resolve (works when gitnexus is globally installed)
+    // 3. Fall back to npx (works when neither is available)
+    let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');
+    if (!fs.existsSync(cliPath)) {
+      try {
+        cliPath = require.resolve('gitnexus/dist/cli/index.js');
+      } catch {
+        cliPath = ''; // will use npx fallback
+      }
     }
+
+    // augment CLI writes result to stderr (KuzuDB's native module captures
+    // stdout fd at OS level, making it unusable in subprocess contexts).
+    const { spawnSync } = require('child_process');
+    let result = '';
+    try {
+      let child;
+      if (cliPath) {
+        child = spawnSync(
+          process.execPath,
+          [cliPath, 'augment', pattern],
+          { encoding: 'utf-8', timeout: 8000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+        );
+      } else {
+        // npx fallback
+        const cmd = process.platform === 'win32' ? 'npx.cmd' : 'npx';
+        child = spawnSync(
+          cmd,
+          ['-y', 'gitnexus', 'augment', pattern],
+          { encoding: 'utf-8', timeout: 15000, cwd, stdio: ['pipe', 'pipe', 'pipe'] }
+        );
+      }
+      result = child.stderr || '';
+    } catch { /* graceful failure */ }
+
+    if (result && result.trim()) {
+      console.log(JSON.stringify({
+        hookSpecificOutput: {
+          hookEventName: 'PreToolUse',
+          additionalContext: result.trim()
+        }
+      }));
+    }
+  } catch (err) {
+    // Graceful failure — log to stderr for debugging
+    console.error('GitNexus hook error:', err.message);
   }
 }
 

gitnexus/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gitnexus",
-  "version": "1.4.8",
+  "version": "1.3.9",
   "description": "Graph-powered code intelligence for AI agents. Index any codebase, query via MCP or CLI.",
   "author": "Abhigyan Patwari",
   "license": "PolyForm-Noncommercial-1.0.0",
@@ -20,7 +20,6 @@
     "knowledge-graph",
     "cursor",
     "claude",
-    "codex",
     "ai-agent",
     "gitnexus",
     "static-analysis",
@@ -40,18 +39,16 @@
   "scripts": {
     "build": "tsc",
     "dev": "tsx watch src/cli/index.ts",
-    "test": "vitest run",
-    "test:unit": "vitest run test/unit",
+    "test": "vitest run test/unit",
     "test:integration": "vitest run test/integration",
+    "test:all": "vitest run",
     "test:watch": "vitest",
     "test:coverage": "vitest run --coverage",
     "prepare": "npm run build",
-    "postinstall": "node scripts/patch-tree-sitter-swift.cjs",
-    "prepack": "npm run build && chmod +x dist/cli/index.js"
+    "postinstall": "node scripts/patch-tree-sitter-swift.cjs"
   },
   "dependencies": {
     "@huggingface/transformers": "^3.0.0",
-    "@ladybugdb/core": "^0.15.2",
     "@modelcontextprotocol/sdk": "^1.0.0",
     "cli-progress": "^3.12.0",
     "commander": "^12.0.0",
@@ -61,10 +58,9 @@
     "graphology": "^0.25.4",
     "graphology-indices": "^0.17.0",
     "graphology-utils": "^2.3.0",
-    "ignore": "^7.0.5",
+    "kuzu": "^0.11.3",
     "lru-cache": "^11.0.0",
     "mnemonist": "^0.39.0",
-    "onnxruntime-node": "^1.24.0",
     "pandemonium": "^2.4.0",
     "tree-sitter": "^0.21.0",
     "tree-sitter-c": "^0.21.0",
@@ -73,15 +69,14 @@
     "tree-sitter-go": "^0.21.0",
     "tree-sitter-java": "^0.21.0",
     "tree-sitter-javascript": "^0.21.0",
+    "tree-sitter-kotlin": "^0.3.8",
     "tree-sitter-php": "^0.23.12",
     "tree-sitter-python": "^0.21.0",
-    "tree-sitter-ruby": "^0.23.1",
     "tree-sitter-rust": "^0.21.0",
     "tree-sitter-typescript": "^0.21.0",
     "uuid": "^13.0.0"
   },
   "optionalDependencies": {
-    "tree-sitter-kotlin": "^0.3.8",
     "tree-sitter-swift": "^0.6.0"
   },
   "devDependencies": {
@@ -91,16 +86,10 @@
     "@types/node": "^20.0.0",
     "@types/uuid": "^10.0.0",
     "@vitest/coverage-v8": "^4.0.18",
-    "husky": "^9.1.7",
     "tsx": "^4.0.0",
     "typescript": "^5.4.5",
     "vitest": "^4.0.18"
   },
-  "overrides": {
-    "@huggingface/transformers": {
-      "onnxruntime-node": "$onnxruntime-node"
-    }
-  },
   "engines": {
     "node": ">=18.0.0"
   }

gitnexus/skills/gitnexus-cli.md

@@ -22,7 +22,7 @@ Run from the project root. This parses all source files, builds the knowledge gr
 | `--force`      | Force full re-index even if up to date                           |
 | `--embeddings` | Enable embedding generation for semantic search (off by default) |
 
-**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale. In Claude Code, a PostToolUse hook runs `analyze` automatically after `git commit` and `git merge`, preserving embeddings if previously generated.
+**When to run:** First time in a project, after major code changes, or when `gitnexus://repo/{name}/context` reports the index is stale.
 
 ### status — Check index freshness
 

gitnexus/src/cli/ai-context.ts

@@ -2,14 +2,13 @@
  * AI Context Generator
  * 
  * Creates AGENTS.md and CLAUDE.md with full inline GitNexus context.
- * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Codex, Cline, etc.
+ * AGENTS.md is the standard read by Cursor, Windsurf, OpenCode, Cline, etc.
  * CLAUDE.md is for Claude Code which only reads that file.
  */
 
 import fs from 'fs/promises';
 import path from 'path';
 import { fileURLToPath } from 'url';
-import { type GeneratedSkillInfo } from './skill-gen.js';
 
 // ESM equivalent of __dirname
 const __filename = fileURLToPath(import.meta.url);
@@ -38,22 +37,7 @@ const GITNEXUS_END_MARKER = '<!-- gitnexus:end -->';
  * - Exact tool commands with parameters — vague directives get ignored
  * - Self-review checklist — forces model to verify its own work
  */
-function generateGitNexusContent(projectName: string, stats: RepoStats, generatedSkills?: GeneratedSkillInfo[]): string {
-  const generatedRows = (generatedSkills && generatedSkills.length > 0)
-    ? generatedSkills.map(s =>
-        `| Work in the ${s.label} area (${s.symbolCount} symbols) | \`.claude/skills/generated/${s.name}/SKILL.md\` |`
-      ).join('\n')
-    : '';
-
-  const skillsTable = `| Task | Read this skill file |
-|------|---------------------|
-| Understand architecture / "How does X work?" | \`.claude/skills/gitnexus/gitnexus-exploring/SKILL.md\` |
-| Blast radius / "What breaks if I change X?" | \`.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md\` |
-| Trace bugs / "Why is X failing?" | \`.claude/skills/gitnexus/gitnexus-debugging/SKILL.md\` |
-| Rename / extract / split / refactor | \`.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md\` |
-| Tools, resources, schema reference | \`.claude/skills/gitnexus/gitnexus-guide/SKILL.md\` |
-| Index, status, clean, wiki CLI commands | \`.claude/skills/gitnexus/gitnexus-cli/SKILL.md\` |${generatedRows ? '\n' + generatedRows : ''}`;
-
+function generateGitNexusContent(projectName: string, stats: RepoStats): string {
   return `${GITNEXUS_START_MARKER}
 # GitNexus — Code Intelligence
 
@@ -125,27 +109,11 @@ Before completing any code modification task, verify:
 3. \`gitnexus_detect_changes()\` confirms changes match expected scope
 4. All d=1 (WILL BREAK) dependents were updated
 
-## Keeping the Index Fresh
-
-After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:
-
-\`\`\`bash
-npx gitnexus analyze
-\`\`\`
-
-If the index previously included embeddings, preserve them by adding \`--embeddings\`:
-
-\`\`\`bash
-npx gitnexus analyze --embeddings
-\`\`\`
-
-To check whether embeddings exist, inspect \`.gitnexus/meta.json\` — the \`stats.embeddings\` field shows the count (0 means no embeddings). **Running analyze without \`--embeddings\` will delete any previously generated embeddings.**
-
-> Claude Code users: A PostToolUse hook handles this automatically after \`git commit\` and \`git merge\`.
-
 ## CLI
 
-${skillsTable}
+- Re-index: \`npx gitnexus analyze\`
+- Check freshness: \`npx gitnexus status\`
+- Generate docs: \`npx gitnexus wiki\`
 
 ${GITNEXUS_END_MARKER}`;
 }
@@ -284,10 +252,9 @@ export async function generateAIContextFiles(
   repoPath: string,
   _storagePath: string,
   projectName: string,
-  stats: RepoStats,
-  generatedSkills?: GeneratedSkillInfo[]
+  stats: RepoStats
 ): Promise<{ files: string[] }> {
-  const content = generateGitNexusContent(projectName, stats, generatedSkills);
+  const content = generateGitNexusContent(projectName, stats);
   const createdFiles: string[] = [];
 
   // Create AGENTS.md (standard for Cursor, Windsurf, OpenCode, Cline, etc.)
@@ -308,3 +275,4 @@ export async function generateAIContextFiles(
 
   return { files: createdFiles };
 }
+

gitnexus/src/cli/analyze.ts

@@ -9,15 +9,14 @@ import { execFileSync } from 'child_process';
 import v8 from 'v8';
 import cliProgress from 'cli-progress';
 import { runPipelineFromRepo } from '../core/ingestion/pipeline.js';
-import { initLbug, loadGraphToLbug, getLbugStats, executeQuery, executeWithReusedStatement, closeLbug, createFTSIndex, loadCachedEmbeddings } from '../core/lbug/lbug-adapter.js';
+import { initKuzu, loadGraphToKuzu, getKuzuStats, executeQuery, executeWithReusedStatement, closeKuzu, createFTSIndex, loadCachedEmbeddings } from '../core/kuzu/kuzu-adapter.js';
 // Embedding imports are lazy (dynamic import) so onnxruntime-node is never
 // loaded when embeddings are not requested. This avoids crashes on Node
 // versions whose ABI is not yet supported by the native binary (#89).
 // disposeEmbedder intentionally not called — ONNX Runtime segfaults on cleanup (see #38)
-import { getStoragePaths, saveMeta, loadMeta, addToGitignore, registerRepo, getGlobalRegistryPath, cleanupOldKuzuFiles } from '../storage/repo-manager.js';
-import { getCurrentCommit, getGitRoot, hasGitDir } from '../storage/git.js';
+import { getStoragePaths, saveMeta, loadMeta, addToGitignore, registerRepo, getGlobalRegistryPath } from '../storage/repo-manager.js';
+import { getCurrentCommit, isGitRepo, getGitRoot } from '../storage/git.js';
 import { generateAIContextFiles } from './ai-context.js';
-import { generateSkillFiles, type GeneratedSkillInfo } from './skill-gen.js';
 import fs from 'fs/promises';
 
 
@@ -46,10 +45,6 @@ function ensureHeap(): boolean {
 export interface AnalyzeOptions {
   force?: boolean;
   embeddings?: boolean;
-  skills?: boolean;
-  verbose?: boolean;
-  /** Index the folder even when no .git directory is present. */
-  skipGit?: boolean;
 }
 
 /** Threshold: auto-skip embeddings for repos with more nodes than this */
@@ -65,7 +60,7 @@ const PHASE_LABELS: Record<string, string> = {
   communities: 'Detecting communities',
   processes: 'Detecting processes',
   complete: 'Pipeline complete',
-  lbug: 'Loading into LadybugDB',
+  kuzu: 'Loading into KuzuDB',
   fts: 'Creating search indexes',
   embeddings: 'Generating embeddings',
   done: 'Done',
@@ -77,10 +72,6 @@ export const analyzeCommand = async (
 ) => {
   if (ensureHeap()) return;
 
-  if (options?.verbose) {
-    process.env.GITNEXUS_VERBOSE = '1';
-  }
-
   console.log('\n  GitNexus Analyzer\n');
 
   let repoPath: string;
@@ -89,50 +80,26 @@ export const analyzeCommand = async (
   } else {
     const gitRoot = getGitRoot(process.cwd());
     if (!gitRoot) {
-      if (!options?.skipGit) {
-        console.log('  Not inside a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n');
-        process.exitCode = 1;
-        return;
-      }
-      // --skip-git: fall back to cwd as the root
-      repoPath = path.resolve(process.cwd());
-    } else {
-      repoPath = gitRoot;
+      console.log('  Not inside a git repository\n');
+      process.exitCode = 1;
+      return;
     }
+    repoPath = gitRoot;
   }
 
-  const repoHasGit = hasGitDir(repoPath);
-  if (!repoHasGit && !options?.skipGit) {
-    console.log('  Not a git repository.\n  Tip: pass --skip-git to index any folder without a .git directory.\n');
+  if (!isGitRepo(repoPath)) {
+    console.log('  Not a git repository\n');
     process.exitCode = 1;
     return;
   }
-  if (!repoHasGit) {
-    console.log('  Warning: no .git directory found \u2014 commit-tracking and incremental updates disabled.\n');
-  }
 
-  const { storagePath, lbugPath } = getStoragePaths(repoPath);
-
-  // Clean up stale KuzuDB files from before the LadybugDB migration.
-  // If kuzu existed but lbug doesn't, we're doing a migration re-index — say so.
-  const kuzuResult = await cleanupOldKuzuFiles(storagePath);
-  if (kuzuResult.found && kuzuResult.needsReindex) {
-    console.log('  Migrating from KuzuDB to LadybugDB — rebuilding index...\n');
-  }
-
-  const currentCommit = repoHasGit ? getCurrentCommit(repoPath) : '';
+  const { storagePath, kuzuPath } = getStoragePaths(repoPath);
+  const currentCommit = getCurrentCommit(repoPath);
   const existingMeta = await loadMeta(storagePath);
 
-  if (existingMeta && !options?.force && !options?.skills && existingMeta.lastCommit === currentCommit) {
-    // Non-git folders have currentCommit = '' — always rebuild since we can't detect changes
-    if (currentCommit !== '') {
-      console.log('  Already up to date\n');
-      return;
-    }
-  }
-
-  if (process.env.GITNEXUS_NO_GITIGNORE) {
-    console.log('  GITNEXUS_NO_GITIGNORE is set — skipping .gitignore (still reading .gitnexusignore)\n');
+  if (existingMeta && !options?.force && existingMeta.lastCommit === currentCommit) {
+    console.log('  Already up to date\n');
+    return;
   }
 
   // Single progress bar for entire pipeline
@@ -156,7 +123,7 @@ export const analyzeCommand = async (
     aborted = true;
     bar.stop();
     console.log('\n  Interrupted — cleaning up...');
-    closeLbug().catch(() => {}).finally(() => process.exit(130));
+    closeKuzu().catch(() => {}).finally(() => process.exit(130));
   };
   process.on('SIGINT', sigintHandler);
 
@@ -206,13 +173,13 @@ export const analyzeCommand = async (
   if (options?.embeddings && existingMeta && !options?.force) {
     try {
       updateBar(0, 'Caching embeddings...');
-      await initLbug(lbugPath);
+      await initKuzu(kuzuPath);
       const cached = await loadCachedEmbeddings();
       cachedEmbeddingNodeIds = cached.embeddingNodeIds;
       cachedEmbeddings = cached.embeddings;
-      await closeLbug();
+      await closeKuzu();
     } catch {
-      try { await closeLbug(); } catch {}
+      try { await closeKuzu(); } catch {}
     }
   }
 
@@ -223,25 +190,25 @@ export const analyzeCommand = async (
     updateBar(scaled, phaseLabel);
   });
 
-  // ── Phase 2: LadybugDB (60–85%) ──────────────────────────────────────
-  updateBar(60, 'Loading into LadybugDB...');
+  // ── Phase 2: KuzuDB (60–85%) ──────────────────────────────────────
+  updateBar(60, 'Loading into KuzuDB...');
 
-  await closeLbug();
-  const lbugFiles = [lbugPath, `${lbugPath}.wal`, `${lbugPath}.lock`];
-  for (const f of lbugFiles) {
+  await closeKuzu();
+  const kuzuFiles = [kuzuPath, `${kuzuPath}.wal`, `${kuzuPath}.lock`];
+  for (const f of kuzuFiles) {
     try { await fs.rm(f, { recursive: true, force: true }); } catch {}
   }
 
-  const t0Lbug = Date.now();
-  await initLbug(lbugPath);
-  let lbugMsgCount = 0;
-  const lbugResult = await loadGraphToLbug(pipelineResult.graph, pipelineResult.repoPath, storagePath, (msg) => {
-    lbugMsgCount++;
-    const progress = Math.min(84, 60 + Math.round((lbugMsgCount / (lbugMsgCount + 10)) * 24));
+  const t0Kuzu = Date.now();
+  await initKuzu(kuzuPath);
+  let kuzuMsgCount = 0;
+  const kuzuResult = await loadGraphToKuzu(pipelineResult.graph, pipelineResult.repoPath, storagePath, (msg) => {
+    kuzuMsgCount++;
+    const progress = Math.min(84, 60 + Math.round((kuzuMsgCount / (kuzuMsgCount + 10)) * 24));
     updateBar(progress, msg);
   });
-  const lbugTime = ((Date.now() - t0Lbug) / 1000).toFixed(1);
-  const lbugWarnings = lbugResult.warnings;
+  const kuzuTime = ((Date.now() - t0Kuzu) / 1000).toFixed(1);
+  const kuzuWarnings = kuzuResult.warnings;
 
   // ── Phase 3: FTS (85–90%) ─────────────────────────────────────────
   updateBar(85, 'Creating search indexes...');
@@ -260,32 +227,22 @@ export const analyzeCommand = async (
 
   // ── Phase 3.5: Re-insert cached embeddings ────────────────────────
   if (cachedEmbeddings.length > 0) {
-    // Check if cached embedding dimensions match current schema
-    const cachedDims = cachedEmbeddings[0].embedding.length;
-    const { EMBEDDING_DIMS } = await import('../core/lbug/schema.js');
-    if (cachedDims !== EMBEDDING_DIMS) {
-      // Dimensions changed (e.g. switched embedding model) — discard cache and re-embed all
-      console.error(`⚠️  Embedding dimensions changed (${cachedDims}d → ${EMBEDDING_DIMS}d), discarding cache`);
-      cachedEmbeddings = [];
-      cachedEmbeddingNodeIds = new Set();
-    } else {
-      updateBar(88, `Restoring ${cachedEmbeddings.length} cached embeddings...`);
-      const EMBED_BATCH = 200;
-      for (let i = 0; i < cachedEmbeddings.length; i += EMBED_BATCH) {
-        const batch = cachedEmbeddings.slice(i, i + EMBED_BATCH);
-        const paramsList = batch.map(e => ({ nodeId: e.nodeId, embedding: e.embedding }));
-        try {
-          await executeWithReusedStatement(
-            `CREATE (e:CodeEmbedding {nodeId: $nodeId, embedding: $embedding})`,
-            paramsList,
-          );
-        } catch { /* some may fail if node was removed, that's fine */ }
-      }
+    updateBar(88, `Restoring ${cachedEmbeddings.length} cached embeddings...`);
+    const EMBED_BATCH = 200;
+    for (let i = 0; i < cachedEmbeddings.length; i += EMBED_BATCH) {
+      const batch = cachedEmbeddings.slice(i, i + EMBED_BATCH);
+      const paramsList = batch.map(e => ({ nodeId: e.nodeId, embedding: e.embedding }));
+      try {
+        await executeWithReusedStatement(
+          `CREATE (e:CodeEmbedding {nodeId: $nodeId, embedding: $embedding})`,
+          paramsList,
+        );
+      } catch { /* some may fail if node was removed, that's fine */ }
     }
   }
 
   // ── Phase 4: Embeddings (90–98%) ──────────────────────────────────
-  const stats = await getLbugStats();
+  const stats = await getKuzuStats();
   let embeddingTime = '0.0';
   let embeddingSkipped = true;
   let embeddingSkipReason = 'off (use --embeddings to enable)';
@@ -299,9 +256,7 @@ export const analyzeCommand = async (
   }
 
   if (!embeddingSkipped) {
-    const { isHttpMode } = await import('../core/embeddings/http-client.js');
-    const httpMode = isHttpMode();
-    updateBar(90, httpMode ? 'Connecting to embedding endpoint...' : 'Loading embedding model...');
+    updateBar(90, 'Loading embedding model...');
     const t0Emb = Date.now();
     const { runEmbeddingPipeline } = await import('../core/embeddings/embedding-pipeline.js');
     await runEmbeddingPipeline(
@@ -309,9 +264,7 @@ export const analyzeCommand = async (
       executeWithReusedStatement,
       (progress) => {
         const scaled = 90 + Math.round((progress.percent / 100) * 8);
-        const label = progress.phase === 'loading-model'
-          ? (httpMode ? 'Connecting to embedding endpoint...' : 'Loading embedding model...')
-          : `Embedding ${progress.nodesProcessed || 0}/${progress.totalNodes || '?'}`;
+        const label = progress.phase === 'loading-model' ? 'Loading embedding model...' : `Embedding ${progress.nodesProcessed || 0}/${progress.totalNodes || '?'}`;
         updateBar(scaled, label);
       },
       {},
@@ -323,13 +276,6 @@ export const analyzeCommand = async (
   // ── Phase 5: Finalize (98–100%) ───────────────────────────────────
   updateBar(98, 'Saving metadata...');
 
-  // Count embeddings in the index (cached + newly generated)
-  let embeddingCount = 0;
-  try {
-    const embResult = await executeQuery(`MATCH (e:CodeEmbedding) RETURN count(e) AS cnt`);
-    embeddingCount = embResult?.[0]?.cnt ?? 0;
-  } catch { /* table may not exist if embeddings never ran */ }
-
   const meta = {
     repoPath,
     lastCommit: currentCommit,
@@ -340,17 +286,11 @@ export const analyzeCommand = async (
       edges: stats.edges,
       communities: pipelineResult.communityResult?.stats.totalCommunities,
       processes: pipelineResult.processResult?.stats.totalProcesses,
-      embeddings: embeddingCount,
     },
   };
   await saveMeta(storagePath, meta);
   await registerRepo(repoPath, meta);
-  // Only attempt to update .gitignore when a .git directory is present.
-  // Use hasGitDir (filesystem check) rather than git CLI subprocess
-  // so we skip correctly for --skip-git folders even if git CLI is available.
-  if (hasGitDir(repoPath)) {
-    await addToGitignore(repoPath);
-  }
+  await addToGitignore(repoPath);
 
   const projectName = path.basename(repoPath);
   let aggregatedClusterCount = 0;
@@ -363,13 +303,6 @@ export const analyzeCommand = async (
     aggregatedClusterCount = Array.from(groups.values()).filter(count => count >= 5).length;
   }
 
-  let generatedSkills: GeneratedSkillInfo[] = [];
-  if (options?.skills && pipelineResult.communityResult) {
-    updateBar(99, 'Generating skill files...');
-    const skillResult = await generateSkillFiles(repoPath, projectName, pipelineResult);
-    generatedSkills = skillResult.skills;
-  }
-
   const aiContext = await generateAIContextFiles(repoPath, storagePath, projectName, {
     files: pipelineResult.totalFileCount,
     nodes: stats.nodes,
@@ -377,9 +310,9 @@ export const analyzeCommand = async (
     communities: pipelineResult.communityResult?.stats.totalCommunities,
     clusters: aggregatedClusterCount,
     processes: pipelineResult.processResult?.stats.totalProcesses,
-  }, generatedSkills);
+  });
 
-  await closeLbug();
+  await closeKuzu();
   // Note: we intentionally do NOT call disposeEmbedder() here.
   // ONNX Runtime's native cleanup segfaults on macOS and some Linux configs.
   // Since the process exits immediately after, Node.js reclaims everything.
@@ -400,7 +333,7 @@ export const analyzeCommand = async (
   const embeddingsCached = cachedEmbeddings.length > 0;
   console.log(`\n  Repository indexed successfully (${totalTime}s)${embeddingsCached ? ` [${cachedEmbeddings.length} embeddings cached]` : ''}\n`);
   console.log(`  ${stats.nodes.toLocaleString()} nodes | ${stats.edges.toLocaleString()} edges | ${pipelineResult.communityResult?.stats.totalCommunities || 0} clusters | ${pipelineResult.processResult?.stats.totalProcesses || 0} flows`);
-  console.log(`  LadybugDB ${lbugTime}s | FTS ${ftsTime}s | Embeddings ${embeddingSkipped ? embeddingSkipReason : embeddingTime + 's'}`);
+  console.log(`  KuzuDB ${kuzuTime}s | FTS ${ftsTime}s | Embeddings ${embeddingSkipped ? embeddingSkipReason : embeddingTime + 's'}`);
   console.log(`  ${repoPath}`);
 
   if (aiContext.files.length > 0) {
@@ -408,12 +341,12 @@ export const analyzeCommand = async (
   }
 
   // Show a quiet summary if some edge types needed fallback insertion
-  if (lbugWarnings.length > 0) {
-    const totalFallback = lbugWarnings.reduce((sum, w) => {
+  if (kuzuWarnings.length > 0) {
+    const totalFallback = kuzuWarnings.reduce((sum, w) => {
       const m = w.match(/\((\d+) edges\)/);
       return sum + (m ? parseInt(m[1]) : 0);
     }, 0);
-    console.log(`  Note: ${totalFallback} edges across ${lbugWarnings.length} types inserted via fallback (schema will be updated in next release)`);
+    console.log(`  Note: ${totalFallback} edges across ${kuzuWarnings.length} types inserted via fallback (schema will be updated in next release)`);
   }
 
   try {
@@ -424,7 +357,7 @@ export const analyzeCommand = async (
 
   console.log('');
 
-  // LadybugDB's native module holds open handles that prevent Node from exiting.
+  // KuzuDB's native module holds open handles that prevent Node from exiting.
   // ONNX Runtime also registers native atexit hooks that segfault on some
   // platforms (#38, #40). Force-exit to ensure clean termination.
   process.exit(0);

gitnexus/src/cli/augment.ts

@@ -23,7 +23,7 @@ export async function augmentCommand(pattern: string): Promise<void> {
     
     if (result) {
       // IMPORTANT: Write to stderr, NOT stdout.
-      // LadybugDB's native module captures stdout fd at OS level during init,
+      // KuzuDB's native module captures stdout fd at OS level during init,
       // which makes stdout permanently broken in subprocess contexts.
       // stderr is never captured, so it works reliably everywhere.
       // The hook reads from the subprocess's stderr.

gitnexus/src/cli/eval-server.ts

@@ -1,7 +1,7 @@
 /**
  * Eval Server — Lightweight HTTP server for SWE-bench evaluation
  * 
- * Keeps LadybugDB warm in memory so tool calls from the agent are near-instant.
+ * Keeps KuzuDB warm in memory so tool calls from the agent are near-instant.
  * Designed to run inside Docker containers during SWE-bench evaluation.
  * 
  * KEY DESIGN: Returns LLM-friendly text, not raw JSON.
@@ -25,7 +25,6 @@
  */
 
 import http from 'http';
-import { writeSync } from 'node:fs';
 import { LocalBackend } from '../mcp/local/local-backend.js';
 
 export interface EvalServerOptions {
@@ -143,10 +142,7 @@ export function formatContextResult(result: any): string {
 }
 
 export function formatImpactResult(result: any): string {
-  if (result.error) {
-    const suggestion = result.suggestion ? `\nSuggestion: ${result.suggestion}` : '';
-    return `Error: ${result.error}${suggestion}`;
-  }
+  if (result.error) return `Error: ${result.error}`;
 
   const target = result.target;
   const direction = result.direction;
@@ -159,11 +155,7 @@ export function formatImpactResult(result: any): string {
 
   const lines: string[] = [];
   const dirLabel = direction === 'upstream' ? 'depends on this (will break if changed)' : 'this depends on';
-  lines.push(`Blast radius for ${target?.kind || ''} ${target?.name} (${direction}): ${total} symbol(s) ${dirLabel}`);
-  if (result.partial) {
-    lines.push('⚠️  Partial results — graph traversal was interrupted. Deeper impacts may exist.');
-  }
-  lines.push('');
+  lines.push(`Blast radius for ${target?.kind || ''} ${target?.name} (${direction}): ${total} symbol(s) ${dirLabel}\n`);
 
   const depthLabels: Record<number, string> = {
     1: 'WILL BREAK (direct)',
@@ -409,10 +401,9 @@ export async function evalServerCommand(options?: EvalServerOptions): Promise<vo
       console.error(`  Auto-shutdown after ${idleTimeoutSec}s idle`);
     }
     try {
-      // Use fd 1 directly — LadybugDB captures process.stdout (#324)
-      writeSync(1, `GITNEXUS_EVAL_SERVER_READY:${port}\n`);
+      process.stdout.write(`GITNEXUS_EVAL_SERVER_READY:${port}\n`);
     } catch {
-      // stdout may not be available (e.g., broken pipe)
+      // stdout may not be available
     }
   });
 

gitnexus/src/cli/index.ts

@@ -4,9 +4,18 @@
 // Removing it from here improves MCP server startup time significantly.
 
 import { Command } from 'commander';
+import { analyzeCommand } from './analyze.js';
+import { serveCommand } from './serve.js';
+import { listCommand } from './list.js';
+import { statusCommand } from './status.js';
+import { mcpCommand } from './mcp.js';
+import { cleanCommand } from './clean.js';
+import { setupCommand } from './setup.js';
+import { augmentCommand } from './augment.js';
+import { wikiCommand } from './wiki.js';
+import { queryCommand, contextCommand, impactCommand, cypherCommand } from './tool.js';
+import { evalServerCommand } from './eval-server.js';
 import { createRequire } from 'node:module';
-import { createLazyAction } from './lazy-action.js';
-
 const _require = createRequire(import.meta.url);
 const pkg = _require('../../package.json');
 const program = new Command();
@@ -18,49 +27,44 @@ program
 
 program
   .command('setup')
-  .description('One-time setup: configure MCP for Cursor, Claude Code, OpenCode, Codex')
-  .action(createLazyAction(() => import('./setup.js'), 'setupCommand'));
-
+  .description('One-time setup: configure MCP for Cursor, Claude Code, OpenCode')
+  .action(setupCommand);
 
 program
   .command('analyze [path]')
   .description('Index a repository (full analysis)')
   .option('-f, --force', 'Force full re-index even if up to date')
   .option('--embeddings', 'Enable embedding generation for semantic search (off by default)')
-  .option('--skills', 'Generate repo-specific skill files from detected communities')
-  .option('--skip-git', 'Index a folder without requiring a .git directory')
-   .option('-v, --verbose', 'Enable verbose ingestion warnings (default: false)')
-   .addHelpText('after', '\nEnvironment variables:\n  GITNEXUS_NO_GITIGNORE=1  Skip .gitignore parsing (still reads .gitnexusignore)')
-   .action(createLazyAction(() => import('./analyze.js'), 'analyzeCommand'));
+  .action(analyzeCommand);
 
 program
   .command('serve')
   .description('Start local HTTP server for web UI connection')
   .option('-p, --port <port>', 'Port number', '4747')
   .option('--host <host>', 'Bind address (default: 127.0.0.1, use 0.0.0.0 for remote access)')
-  .action(createLazyAction(() => import('./serve.js'), 'serveCommand'));
+  .action(serveCommand);
 
 program
   .command('mcp')
   .description('Start MCP server (stdio) — serves all indexed repos')
-  .action(createLazyAction(() => import('./mcp.js'), 'mcpCommand'));
+  .action(mcpCommand);
 
 program
   .command('list')
   .description('List all indexed repositories')
-  .action(createLazyAction(() => import('./list.js'), 'listCommand'));
+  .action(listCommand);
 
 program
   .command('status')
   .description('Show index status for current repo')
-  .action(createLazyAction(() => import('./status.js'), 'statusCommand'));
+  .action(statusCommand);
 
 program
   .command('clean')
   .description('Delete GitNexus index for current repo')
   .option('-f, --force', 'Skip confirmation prompt')
   .option('--all', 'Clean all indexed repos')
-  .action(createLazyAction(() => import('./clean.js'), 'cleanCommand'));
+  .action(cleanCommand);
 
 program
   .command('wiki [path]')
@@ -71,12 +75,12 @@ program
   .option('--api-key <key>', 'LLM API key (saved to ~/.gitnexus/config.json)')
   .option('--concurrency <n>', 'Parallel LLM calls (default: 3)', '3')
   .option('--gist', 'Publish wiki as a public GitHub Gist after generation')
-  .action(createLazyAction(() => import('./wiki.js'), 'wikiCommand'));
+  .action(wikiCommand);
 
 program
   .command('augment <pattern>')
   .description('Augment a search pattern with knowledge graph context (used by hooks)')
-  .action(createLazyAction(() => import('./augment.js'), 'augmentCommand'));
+  .action(augmentCommand);
 
 // ─── Direct Tool Commands (no MCP overhead) ────────────────────────
 // These invoke LocalBackend directly for use in eval, scripts, and CI.
@@ -89,7 +93,7 @@ program
   .option('-g, --goal <text>', 'What you want to find')
   .option('-l, --limit <n>', 'Max processes to return (default: 5)')
   .option('--content', 'Include full symbol source code')
-  .action(createLazyAction(() => import('./tool.js'), 'queryCommand'));
+  .action(queryCommand);
 
 program
   .command('context [name]')
@@ -98,7 +102,7 @@ program
   .option('-u, --uid <uid>', 'Direct symbol UID (zero-ambiguity lookup)')
   .option('-f, --file <path>', 'File path to disambiguate common names')
   .option('--content', 'Include full symbol source code')
-  .action(createLazyAction(() => import('./tool.js'), 'contextCommand'));
+  .action(contextCommand);
 
 program
   .command('impact <target>')
@@ -107,13 +111,13 @@ program
   .option('-r, --repo <name>', 'Target repository')
   .option('--depth <n>', 'Max relationship depth (default: 3)')
   .option('--include-tests', 'Include test files in results')
-  .action(createLazyAction(() => import('./tool.js'), 'impactCommand'));
+  .action(impactCommand);
 
 program
   .command('cypher <query>')
   .description('Execute raw Cypher query against the knowledge graph')
   .option('-r, --repo <name>', 'Target repository')
-  .action(createLazyAction(() => import('./tool.js'), 'cypherCommand'));
+  .action(cypherCommand);
 
 // ─── Eval Server (persistent daemon for SWE-bench) ─────────────────
 
@@ -122,6 +126,6 @@ program
   .description('Start lightweight HTTP server for fast tool calls during evaluation')
   .option('-p, --port <port>', 'Port number', '4848')
   .option('--idle-timeout <seconds>', 'Auto-shutdown after N seconds idle (0 = disabled)', '0')
-  .action(createLazyAction(() => import('./eval-server.js'), 'evalServerCommand'));
+  .action(evalServerCommand);
 
 program.parse(process.argv);

gitnexus/src/cli/lazy-action.ts

@@ -1,26 +0,0 @@
-/**
- * Creates a lazy-loaded CLI action that defers module import until invocation.
- * The generic constraints ensure the export name is a valid key of the module
- * at compile time — catching typos when used with concrete module imports.
- */
-
-function isCallable(value: unknown): value is (...args: unknown[]) => unknown {
-  return typeof value === 'function';
-}
-
-export function createLazyAction<
-  TModule extends Record<string, unknown>,
-  TKey extends string & keyof TModule,
->(
-  loader: () => Promise<TModule>,
-  exportName: TKey,
-): (...args: unknown[]) => Promise<void> {
-  return async (...args: unknown[]): Promise<void> => {
-    const module = await loader();
-    const action = module[exportName];
-    if (!isCallable(action)) {
-      throw new Error(`Lazy action export not found: ${exportName}`);
-    }
-    await action(...args);
-  };
-}

gitnexus/src/cli/mcp.ts

@@ -11,7 +11,7 @@ import { LocalBackend } from '../mcp/local/local-backend.js';
 
 export const mcpCommand = async () => {
   // Prevent unhandled errors from crashing the MCP server process.
-  // LadybugDB lock conflicts and transient errors should degrade gracefully.
+  // KuzuDB lock conflicts and transient errors should degrade gracefully.
   process.on('uncaughtException', (err) => {
     console.error(`GitNexus MCP: uncaught exception — ${err.message}`);
     // Process is in an undefined state after uncaughtException — exit after flushing

gitnexus/src/cli/setup.ts

@@ -9,15 +9,11 @@
 import fs from 'fs/promises';
 import path from 'path';
 import os from 'os';
-import { execFile } from 'child_process';
-import { promisify } from 'util';
 import { fileURLToPath } from 'url';
-import { glob } from 'glob';
 import { getGlobalDir } from '../storage/repo-manager.js';
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
-const execFileAsync = promisify(execFile);
 
 interface SetupResult {
   configured: string[];
@@ -172,18 +168,16 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
       // even when it's no longer inside the npm package tree
       const resolvedCli = path.join(__dirname, '..', 'cli', 'index.js');
       const normalizedCli = path.resolve(resolvedCli).replace(/\\/g, '/');
-      const jsonCli = JSON.stringify(normalizedCli);
       content = content.replace(
         "let cliPath = path.resolve(__dirname, '..', '..', 'dist', 'cli', 'index.js');",
-        `let cliPath = ${jsonCli};`
+        `let cliPath = '${normalizedCli}';`
       );
       await fs.writeFile(dest, content, 'utf-8');
     } catch {
       // Script not found in source — skip
     }
 
-    const hookPath = path.join(destHooksDir, 'gitnexus-hook.cjs').replace(/\\/g, '/');
-    const hookCmd = `node "${hookPath.replace(/"/g, '\\"')}"`;
+    const hookCmd = `node "${path.join(destHooksDir, 'gitnexus-hook.cjs').replace(/\\/g, '/')}"`;
 
     // Merge hook config into ~/.claude/settings.json
     const existing = await readJsonFile(settingsPath) || {};
@@ -192,31 +186,25 @@ async function installClaudeCodeHooks(result: SetupResult): Promise<void> {
     // NOTE: SessionStart hooks are broken on Windows (Claude Code bug #23576).
     // Session context is delivered via CLAUDE.md / skills instead.
 
-    // Helper: add a hook entry if one with 'gitnexus-hook' isn't already registered
-    interface HookEntry { hooks?: Array<{ command?: string }> }
-    function ensureHookEntry(
-      eventName: string,
-      matcher: string,
-      timeout: number,
-      statusMessage: string,
-    ) {
-      if (!existing.hooks[eventName]) existing.hooks[eventName] = [];
-      const hasHook = existing.hooks[eventName].some(
-        (h: HookEntry) => h.hooks?.some(hh => hh.command?.includes('gitnexus-hook'))
-      );
-      if (!hasHook) {
-        existing.hooks[eventName].push({
-          matcher,
-          hooks: [{ type: 'command', command: hookCmd, timeout, statusMessage }],
-        });
-      }
+    // Add PreToolUse hook if not already present
+    if (!existing.hooks.PreToolUse) existing.hooks.PreToolUse = [];
+    const hasPreToolHook = existing.hooks.PreToolUse.some(
+      (h: any) => h.hooks?.some((hh: any) => hh.command?.includes('gitnexus'))
+    );
+    if (!hasPreToolHook) {
+      existing.hooks.PreToolUse.push({
+        matcher: 'Grep|Glob|Bash',
+        hooks: [{
+          type: 'command',
+          command: hookCmd,
+          timeout: 8000,
+          statusMessage: 'Enriching with GitNexus graph context...',
+        }],
+      });
     }
 
-    ensureHookEntry('PreToolUse', 'Grep|Glob|Bash', 10, 'Enriching with GitNexus graph context...');
-    ensureHookEntry('PostToolUse', 'Bash', 10, 'Checking GitNexus index freshness...');
-
     await writeJsonFile(settingsPath, existing);
-    result.configured.push('Claude Code hooks (PreToolUse, PostToolUse)');
+    result.configured.push('Claude Code hooks (PreToolUse)');
   } catch (err: any) {
     result.errors.push(`Claude Code hooks: ${err.message}`);
   }
@@ -242,75 +230,14 @@ async function setupOpenCode(result: SetupResult): Promise<void> {
   }
 }
 
-/**
- * Build a TOML section for Codex MCP config (~/.codex/config.toml).
- */
-function getCodexMcpTomlSection(): string {
-  const entry = getMcpEntry();
-  const command = JSON.stringify(entry.command);
-  const args = `[${entry.args.map(arg => JSON.stringify(arg)).join(', ')}]`;
-  return `[mcp_servers.gitnexus]\ncommand = ${command}\nargs = ${args}\n`;
-}
-
-/**
- * Append GitNexus MCP server config to Codex's config.toml if missing.
- */
-async function upsertCodexConfigToml(configPath: string): Promise<void> {
-  let existing = '';
-  try {
-    existing = await fs.readFile(configPath, 'utf-8');
-  } catch {
-    existing = '';
-  }
-
-  if (existing.includes('[mcp_servers.gitnexus]')) {
-    return;
-  }
-
-  const section = getCodexMcpTomlSection();
-  const nextContent = existing.trim().length > 0
-    ? `${existing.trimEnd()}\n\n${section}`
-    : section;
-
-  await fs.mkdir(path.dirname(configPath), { recursive: true });
-  await fs.writeFile(configPath, `${nextContent.trimEnd()}\n`, 'utf-8');
-}
-
-async function setupCodex(result: SetupResult): Promise<void> {
-  const codexDir = path.join(os.homedir(), '.codex');
-  if (!(await dirExists(codexDir))) {
-    result.skipped.push('Codex (not installed)');
-    return;
-  }
-
-  try {
-    const entry = getMcpEntry();
-    await execFileAsync(
-      'codex',
-      ['mcp', 'add', 'gitnexus', '--', entry.command, ...entry.args],
-      { shell: process.platform === 'win32' }
-    );
-    result.configured.push('Codex');
-    return;
-  } catch {
-    // Fallback for environments where `codex` binary isn't on PATH.
-  }
-
-  try {
-    const configPath = path.join(codexDir, 'config.toml');
-    await upsertCodexConfigToml(configPath);
-    result.configured.push('Codex (MCP added to ~/.codex/config.toml)');
-  } catch (err: any) {
-    result.errors.push(`Codex: ${err.message}`);
-  }
-}
-
 // ─── Skill Installation ───────────────────────────────────────────
 
+const SKILL_NAMES = ['gitnexus-exploring', 'gitnexus-debugging', 'gitnexus-impact-analysis', 'gitnexus-refactoring', 'gitnexus-guide', 'gitnexus-cli'];
+
 /**
  * Install GitNexus skills to a target directory.
  * Each skill is installed as {targetDir}/gitnexus-{skillName}/SKILL.md
- * following the Agent Skills standard (Cursor, Claude Code, and Codex).
+ * following the Agent Skills standard (both Cursor and Claude Code).
  *
  * Supports two source layouts:
  *   - Flat file:  skills/{name}.md           → copied as SKILL.md
@@ -320,38 +247,25 @@ async function installSkillsTo(targetDir: string): Promise<string[]> {
   const installed: string[] = [];
   const skillsRoot = path.join(__dirname, '..', '..', 'skills');
 
-  let flatFiles: string[] = [];
-  let dirSkillFiles: string[] = [];
-  try {
-    [flatFiles, dirSkillFiles] = await Promise.all([
-      glob('*.md', { cwd: skillsRoot }),
-      glob('*/SKILL.md', { cwd: skillsRoot }),
-    ]);
-  } catch {
-    return [];
-  }
-
-  const skillSources = new Map<string, { isDirectory: boolean }>();
-
-  for (const relPath of dirSkillFiles) {
-    skillSources.set(path.dirname(relPath), { isDirectory: true });
-  }
-  for (const relPath of flatFiles) {
-    const skillName = path.basename(relPath, '.md');
-    if (!skillSources.has(skillName)) {
-      skillSources.set(skillName, { isDirectory: false });
-    }
-  }
-
-  for (const [skillName, source] of skillSources) {
+  for (const skillName of SKILL_NAMES) {
     const skillDir = path.join(targetDir, skillName);
 
     try {
-      if (source.isDirectory) {
-        const dirSource = path.join(skillsRoot, skillName);
+      // Try directory-based skill first (skills/{name}/SKILL.md)
+      const dirSource = path.join(skillsRoot, skillName);
+      const dirSkillFile = path.join(dirSource, 'SKILL.md');
+
+      let isDirectory = false;
+      try {
+        const stat = await fs.stat(dirSource);
+        isDirectory = stat.isDirectory();
+      } catch { /* not a directory */ }
+
+      if (isDirectory) {
         await copyDirRecursive(dirSource, skillDir);
         installed.push(skillName);
       } else {
+        // Fall back to flat file (skills/{name}.md)
         const flatSource = path.join(skillsRoot, `${skillName}.md`);
         const content = await fs.readFile(flatSource, 'utf-8');
         await fs.mkdir(skillDir, { recursive: true });
@@ -419,24 +333,6 @@ async function installOpenCodeSkills(result: SetupResult): Promise<void> {
   }
 }
 
-/**
- * Install global Codex skills to ~/.agents/skills/gitnexus/
- */
-async function installCodexSkills(result: SetupResult): Promise<void> {
-  const codexDir = path.join(os.homedir(), '.codex');
-  if (!(await dirExists(codexDir))) return;
-
-  const skillsDir = path.join(os.homedir(), '.agents', 'skills');
-  try {
-    const installed = await installSkillsTo(skillsDir);
-    if (installed.length > 0) {
-      result.configured.push(`Codex skills (${installed.length} skills → ~/.agents/skills/)`);
-    }
-  } catch (err: any) {
-    result.errors.push(`Codex skills: ${err.message}`);
-  }
-}
-
 // ─── Main command ──────────────────────────────────────────────────
 
 export const setupCommand = async () => {
@@ -459,14 +355,12 @@ export const setupCommand = async () => {
   await setupCursor(result);
   await setupClaudeCode(result);
   await setupOpenCode(result);
-  await setupCodex(result);
   
   // Install global skills for platforms that support them
   await installClaudeCodeSkills(result);
   await installClaudeCodeHooks(result);
   await installCursorSkills(result);
   await installOpenCodeSkills(result);
-  await installCodexSkills(result);
 
   // Print results
   if (result.configured.length > 0) {