9c24e3459e
* fix(rust): let the qualified-call filter see inline modules The negative filter added in #2741 builds its set of known module names from FILE PATHS, so an inline `mod x { … }` — which appears in no path — was absent from it. Every module-qualified call into an inline module was therefore rejected before any candidate channel ran, which is a hole in that optimisation rather than in the resolution logic it guards. The per-pass index now unions the file-derived names with inline module names taken from the scope model: a `mod` declaration binds a `Namespace` def locally in the declaring scope, and that binding is the only place an inline module's name exists. Collected in the same walk that already builds the module → scope map, so it costs no extra pass. Found while fixing #2742, where a correctly resolved call into `mod inner { … }` still could not reach its target. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01J5nWP4BFeBSjbQ3uqAjtxV * fix(scope-resolution): try the namespace-prefixed node key before the bare one `resolveDefGraphId` looked up the plain `qualifiedName` key first and only retried with the `namespacePrefix`-qualified key afterwards. For the defs that carry a prefix the qualified name is a bare TAIL, so the plain key happily matched a same-named item at a different namespace depth in the same file and returned it before the more specific retry was ever reached. The namespace-prefixed key is strictly the more specific of the two, so it is now tried first. Where no such node exists the lookup falls through to exactly the previous order, which keeps the #1982 behaviour this retry was added for. Without this, a call into `mod inner { fn dispatch }` resolved to the correct definition and then mapped it onto the crate-root `fn dispatch` node — the self-loop #2742 describes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01J5nWP4BFeBSjbQ3uqAjtxV * fix(rust): qualify items by their enclosing mod chain so same-named ones stay distinct (#2742) Node identity is `<label>:<file>:<qualifiedName>` and carried no module path, so an inline `mod inner { fn dispatch }` and a crate-root `fn dispatch` in the same file collapsed onto `Function:<file>:dispatch`, first-wins. Resolution already picked the right definition — the target simply was not representable, so a correct resolution still rendered as a self-loop and `impact` reported the real callee as unreached. The mechanism already existed: `qualifyRustImplTargetByModScope` has walked `mod_item` ancestors for impl targets since #1982. Generalised to `qualifyByEnclosingModScope` and applied to free items, so `mod inner { fn dispatch }` becomes `Function:<file>:inner.dispatch`. Keyed purely on the `mod_item` node type, exactly as the impl qualifier already was, so it is a no-op for every language whose grammar has no such node. Two constraints found by tests rather than by reading, both now encoded: - The helper normalised `::` to `.` unconditionally. With no enclosing `mod` that rewrote a top-level `impl a::Inner` from `a::Inner` to `a.Inner` and moved its node id away from the one the HAS_METHOD owner edge emits, breaking the #1975 scoped-impl ownership. It now returns raw text untouched when there are no mod segments, which also makes the change strictly additive for every id that has no enclosing module. - Qualification is scoped to items with no enclosing class/impl. A method already carries its owner's name, and that owner's id is mod-scoped by the impl qualifier, so qualifying the method again breaks the same byte-for-byte agreement. Same-named methods on same-named types in sibling modules therefore still collapse — a narrower residual than the free-item case fixed here, and one belonging to the owner edge rather than to this path. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01J5nWP4BFeBSjbQ3uqAjtxV * fix(storage): bump schema versions for the mod-qualified Rust node ids (#2742) `INCREMENTAL_SCHEMA_VERSION` 24 -> 25 and `SCHEMA_BUMP` 31 -> 32. Node ids change for every Rust item inside any `mod` block, and `#[cfg(test)] mod tests` makes that close to every Rust repository. A pre-v25 index therefore holds ids an incremental top-up cannot reconcile — the old nodes would simply be stranded — so the reuse gate has to force a full re-analyze. The qualified name is computed in the parse worker, so a warm parse cache would likewise replay the old unqualified ids and keep the collapse. This branch originally claimed v24; #2708 took that number and merged first, so it is renumbered to v25 here. That is exactly the collision the v29 note in parse-cache.ts warns about, and re-checking against origin/main at rebase time rather than at branch time is what caught it. #2708 did not touch `SCHEMA_BUMP`, so 32 is free. The version-pin test moves with the bump by design, including the new pre-v25 row in the reuse-gate table. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01J5nWP4BFeBSjbQ3uqAjtxV * fix(rust): stop mod-qualifying container ids while their owner edges stay bare (#2745 review) #2742 re-keyed Rust node ids by the enclosing `mod` chain. The mint moved; the owner-edge anchor did not. `findEnclosingClassInfo` mints a member's owner id from the container's BARE `nameNode.text` and only follows a qualified shape when the provider sets `classExtractor.qualifiedNodeId`, which Rust does not. So every `struct` / `trait` / `enum` / `impl` declared directly inside a `mod` got a node id that none of its member edges pointed at. Five lines of idiomatic Rust were enough: pub mod engine { pub struct Config { pub retries: usize } } NODE Struct:src/lib.rs:engine.Config DANGLING HAS_PROPERTY Struct:src/lib.rs:Config -> Property:src/lib.rs:Config.retries The rows are discarded by the IGNORE_ERRORS COPY retry, so the struct silently lost every field. A trait impl inside a `mod` additionally dropped its METHOD_IMPLEMENTS edge outright. The same gap put `impl a::Inner` inside a `mod` back on the #1975 rake that `qualifyByEnclosingModScope`'s own docblock warns about. The impl-target branch deliberately fires only for an UNSCOPED `type_identifier`; the new gate had no such restriction and picked up the scoped targets that branch had just excluded, minting `Impl:<file>:outer.a.Inner` against an anchor still reading `Impl:<file>:a::Inner`. The member side was already excluded via `!enclosingClassInfo`. This adds the owner side, gated on `MEMBER_OWNER_NODE_TYPES` — derived from `CLASS_CONTAINER_TYPES`, which is already the single source of "this node type owns member edges" and already carries an INVARIANT note binding it to `CONTAINER_TYPE_TO_LABEL`. A language adding a container therefore cannot gain a mismatched id shape here without also failing that invariant. Keyed purely on tree-sitter node types, so no language name enters shared ingestion. `union_item` is listed too: its fields are captured as Property but it is not a recognized owner, so they carry no HAS_PROPERTY edge and cannot dangle — it is here so a union's id keeps the same shape as the struct beside it. Containers still collapse across sibling modules, exactly as before this fix. That residual belongs to the owner edge, and is not worked around here. Regression tests use the UNFILTERED `findDanglingEdges(result)`. Every other dangling assertion in `rust.test.ts` passes `['HAS_METHOD']`, which is precisely why the HAS_PROPERTY breakage shipped with a green suite. They assert the NODE id rather than only the edge's anchor, because the anchor was already bare while the bug was live — an edge-only assertion passes in both builds. All four fail when the new gate clause alone is reverted. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * fix(rust): resolve modules nested inside an inline mod (#2745 review) The #2730 self-loop survived one `mod` deeper: pub mod outer { pub mod tools { pub fn dispatch() {} } pub fn dispatch() { tools::dispatch(); } } CALLS outer.dispatch -> outer.dispatch <- the #2730 symptom NODE outer.tools.dispatch <- correct target, unlinked Two gates were blind to a nested inline module, so the hook refused and the shared lexical tier bound the call to the enclosing same-name `dispatch`: `knownModuleNames` was collected by walking `moduleScopeByFile`, which maps a file to its ROOT `Module` scope only. A `mod` nested inside an inline `mod` binds in the parent module's scope, so the walk saw depth-1 inline modules and missed every nested one — `tools` never entered the set and the negative filter rejected the qualifier before any candidate ran. `declaresSubmodule` had the same root-only assumption, so even with the name known the candidate `outer::tools` was never yielded. Both now read the def index. Names come from every `Namespace` def; inline module PATHS are derived from the members' `namespacePrefix` rather than from the `mod` defs, because a `mod` def carries no nesting information of its own — inside `mod outer { mod tools { … } }` the inner def is `qualifiedName: 'tools'` with NO `namespacePrefix`, while every def within it is stamped `outer.tools`. A `Namespace` scope also owns its OWN def rather than its children's, so the scope tree cannot answer this either: the `mod outer` scope lists `outer`, never `tools`. Restricted to non-empty prefixes, so this stays a DECLARATION check. Including file-derived modules would let an undeclared or `cfg`-gated file on disk outrank a real `use` binding — the regression #2741's review already fixed once. File-backed submodules therefore keep going through the binding check. A module with no defs at all is absent from the set, which is harmless: it has no member for a qualified call to resolve to. Cost is one pass over an already-resident def index, memoized per resolution pass on the existing WeakMap — the same order of work as the binding walk it replaces, and it subsumes it. `isLocalNamespaceBinding` was going to single-source the duplicated "locally declared submodule" predicate the review flagged; deriving paths from members removed the second copy outright instead. Regression fixture covers depth 2 and depth 3, so the fix is depth-agnostic rather than depth-2 special-cased. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * fix(rust): let an imported type outrank a same-named module (#2745 review) Widening the negative filter to inline `mod` names let a type-qualified call through whenever a module happened to share the type's name. The crate-root-relative candidate then captured it: // src/lib.rs pub mod Buffer { pub fn with_capacity() -> usize { 111 } } // src/b.rs use crate::c::Buffer; // the real target lives in c.rs pub fn call() -> usize { Buffer::with_capacity() } base: (no CALLS edge — unresolved) PR: CALLS b::call -> Function:src/lib.rs:Buffer.with_capacity <- fabricated `ids.ts` states the doctrine this broke: a missing edge is the correct failure direction for a graph whose consumers include `impact`; a fabricated caller is not. The base produced the missing edge and the PR produced the fabricated one. That third candidate is the loosest of the three — a guess at a crate-root-relative path the caller never wrote, kept for 2015-edition style. In Rust 2018 a bare first segment resolves in the CALLER's module, so a local binding for that segment settles the question: it is now skipped when the head names anything non-module in the caller's own module. Candidates 1 and 2 are untouched, and they run first, so the legitimate `use crate::tools;` path is unaffected. The binding lookup goes through `lookupBindingsAt`. A first attempt read `Scope.bindings` directly and the guard never fired: a `use` binding is finalize OUTPUT and absent from the scope's own local table, which is exactly the imported-type case being guarded. Contract I8 in `contract/scope-resolver.ts` requires that channel anyway. The regression test asserts the forbidden TARGET rather than an empty edge set, and separately asserts the module member still exists as a node — otherwise the test would pass just as well if the call went unresolved for some unrelated reason, or if the module node disappeared entirely. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * fix(scope-resolution): try the namespace-prefixed name on the TAGGED keys too (#2745 review) `resolveDefGraphId` gained a namespace-prefixed retry for the plain qualified key in this PR, but the five tagged keys above it — template constraints, parameter types, parameter shape, arity, template arguments — kept composing from the bare `qualifiedName`. For a namespace- or `mod`-qualified def those keys are simply dead: `node-lookup.ts` registers them under the QUALIFIED name (`inner.dispatch#0`) while this side built `dispatch#0`. The keys exist to separate overloads, so a mod-scoped overload set was relying on whichever later key happened to catch it. Verified as a miss rather than a mis-hit before changing anything — an end-to-end run with a crate-root decoy of the same name and arity binds correctly — so this is hygiene, not a live bug. Worth doing while the code is open rather than leaving five keys dead and the behaviour dependent on fallback order. Both name forms now go through one `lookupTagged` helper, most specific first, so a sixth tagged key cannot be added with the bare form only. That also removes the five hand-repeated `qualifiedKey(...)` / `nodeLookup.get(...)` pairs. Also pins the C++ `EXTENDS` retarget this PR's reorder produces. `cpp-two-phase-dependent-base-cross-ns-deep` declares a global `Inner` decoy alongside `ns::a::b::Inner`; the base's `qualifiedName` is a bare `Inner` with the path on `namespacePrefix`, so only the prefixed key separates them, and only if it runs first. The improvement was riding unasserted in a Rust-scoped PR. The captures golden covers every `rust-*` fixture, so the three fixtures added by this review series drift it; regenerated with UPDATE_GOLDEN=1. Verified: 785 tests across cpp / csharp / rust resolvers and the callable-id-lockstep unit test. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * fix(rust): keep a mod declared inside a fn from hoisting above the callable (#2745 review) `fn wrapper() { mod helper { fn dispatch } }` minted `Function:<file>:helper.wrapper.dispatch@2:8` — the mod segment composed OUTSIDE the enclosing-callable prefix, inverting the real nesting. Nothing dangled: the `@line:col` suffix already makes a function-local callable's id unique, which is also why the mod segment adds no identity in this position. The path simply read as a lie about the source. It is now skipped rather than reordered — interleaving two qualifier passes to fix the order would be real machinery for a shape whose ids are already unique. Also folds in the three documentation and structure findings from the same review: - The 4-clause gate is extracted to a named `qualifiesByEnclosingModScope`, matching the two conditions directly above it in the same function, which were already named consts. - `qualifyByEnclosingModScope`'s docblock documented only the impl-target contract even though the generalized name has had a second, looser caller since #2742. It now states both, and says which gate belongs to which — that gap is what let the #1975 scoped-impl regression through in the first place. - The "cheap rejection BEFORE any index work" comment was no longer true: `passIndexFor` walks the def index on its first call in a pass. Corrected rather than left to mislead the next reader into thinking the filter is free. What it still buys — skipping the per-site candidate search, the part that scales with the workspace — is stated instead. Verified: 279 tests across the Rust resolver suite and the Rust scope-resolution unit tests. Captures golden regenerated for the extended fixture. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * test(storage): move main's SCHEMA_BUMP pin to 32 for the mod-qualified ids (#2745 review) `#2736` added a pin asserting `SCHEMA_BUMP === 31` on main, which arrived on this branch through the merge of main while `0062a5c2` had already bumped the constant to 32. Neither side conflicted textually — the pin and the constant live in different files — so the merge was clean and the test failed instead. That is the pin working as designed: it exists so a bump cannot ride along unnoticed, and this is the fifth time a SCHEMA_BUMP collision has been caught by a guard rather than by review. Updated to 32 with the reason recorded inline. `INCREMENTAL_SCHEMA_VERSION` needs no second bump: 25 was introduced by this unmerged branch, so no released index carries it, and its own pin in `call-summary-schema-version.test.ts` is already consistent. Verified: 119 tests across the parse-cache, schema-version, incremental-orchestration and the two identity suites that arrived with the merge. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z * test(bench): rebaseline the Rust capture fingerprint for the three new fixtures (#2745 review) CI caught what I missed: [scope-capture --check] FAIL: rust: capture fingerprint drift (got 05acbaca..., expected 90fda086...) fixture_count 202 `bench/scope-capture` fingerprints the whole `rust-*` fixture corpus, so the three fixtures added by this review series drift it. I rebaselined the `rust-captures-golden` snapshot and stopped there — a new fixture is a call site of BOTH, and updating only one is how this reached CI red. This is the same class as PR #2743's headline finding, from the other direction: an id-shape change makes every synthetic corpus a call site, and the author fixed the unit-test fixture and missed the bench. Here it is a fixture-count change rather than an id-shape change, and the review that flagged the #2743 lead as "REFUTED, bench/ has no Rust node-id corpus" was right about node ids and wrong about the corpus fingerprint. Noted for the next author in the baseline entry itself. Verified as pure corpus growth rather than a capture-logic shift: removing ONLY the three new fixture directories and re-running reproduces the prior fingerprint exactly (196 fixtures, capture_groups_fp 3432), and restoring them gives the new one (202, 3556). `emitRustScopeCaptures` is untouched by this series. Scaling 1.022 local / 1.057 CI, well inside the 1.5 budget. `bench/python-scope` globs `python-*` only and is unaffected; no other bench walks the Rust corpus. `--check` now PASSes for all 15 languages. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_019GvVxWt1ShhEP8CiMj3b6Z --------- Co-authored-by: Gergo Magyar <gergomagyar0@gmail.com> Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>
GitNexus
⚠️ Important Notice: GitNexus has NO official cryptocurrency, token, or coin. Any token/coin using the GitNexus name on Pump.fun or any other platform is not affiliated with, endorsed by, or created by this project or its maintainers. Do not purchase any cryptocurrency claiming association with GitNexus.
The nervous system for agent context.
Indexes any codebase into a knowledge graph — every dependency, call chain, cluster, and execution flow — then exposes it through smart MCP tools so AI agents never miss code.
💬 Discord · 🌐 Web UI · 🏢 Enterprise (SaaS & self-hosted)
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 — a knowledge graph tracks every relationship, not just descriptions.
TL;DR: The CLI + MCP makes your AI agent reliable — it gives Cursor, Claude Code, Antigravity, 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. The Web UI is a quick way to chat with any repo in the browser.
Quick Start
# 1. Index your repo (run from repo root)
npx gitnexus analyze
# 2. Connect your editors (one-time, auto-detects Claude Code, Cursor, Codex, …)
npx gitnexus setup
That's it. analyze indexes the codebase, installs agent skills, registers Claude Code hooks, and creates AGENTS.md / CLAUDE.md context files — all in one command. setup writes the MCP config so your AI agent can use the graph.
Install problems? npm 11 crash · slow cold install · no C++ toolchain
On npm 11.x?
npxcan crash during install withCannot destructure property 'package' of 'node.target'(an npm/arborist bug, before GitNexus runs). Use pnpm instead — it builds the native deps explicitly:pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyzeOr install globally (
npm install -g gitnexus@latest) and rungitnexus analyze. See #1939.
Fastest MCP startup: install globally (
npm i -g gitnexus) before runninggitnexus setup— this writes an absolute-path MCP config that bypassesnpxentirely. On a cold cache, annpx-based MCP install can exceed Claude Code'sMCP_TIMEOUTdefault (~30s).
No C++ toolchain? Set
GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1beforenpm install -g gitnexusto skip the vendored grammar materialize/build fortree-sitter-dart,tree-sitter-proto,tree-sitter-swift, andtree-sitter-kotlin— those four languages won't be parsed, but install completes in seconds withoutpython3/make/g++. Strict=1only — any other value falls through to the rebuild.
Behind an HTTP proxy / regional firewall?
onnxruntime-node's postinstall downloads optional CUDA binaries fromapi.nuget.organd ignoresHTTP_PROXY/HTTPS_PROXY(#2370). The embedding stack is an optional dependency, so a failed download no longer breaks the install — and it self-heals: the firstgitnexus analyze --embeddings(orgitnexus embeddings install) fetches the stack through your npm registry config (mirrors/proxies apply, no NuGet) into~/.gitnexus/embedding-runtime(override withGITNEXUS_EMBEDDING_RUNTIME_DIR). The on-demand prefix needs Node withmodule.registerHooks(≥ 22.15 on 22.x, ≥ 23.5 on 23.x); on older Node, keep the stack in the install itself withONNXRUNTIME_NODE_INSTALL=skip npm install -g gitnexus(works on every supported Node).
About
tree-sitter-kotlin: like Dart/Proto/Swift, Kotlin is a vendored grammar (undergitnexus/vendor/tree-sitter-kotlin). Upstream ships source only (no prebuilt binaries), so GitNexus cross-builds the platform prebuilds itself (via thebuild-tree-sitter-prebuildsGitHub Actions workflow) and vendors them — the same uniform pipeline used for Dart, Proto, and Swift.node-gyp-buildselects the right.nodeat require time, so no C/C++ toolchain is needed. If no prebuild matches your platform-arch, only Kotlin (.kt/.kts) parsing is unavailable; the rest ofgitnexusis unaffected.
Two Ways to Use GitNexus
| CLI + MCP (recommended) | 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, Antigravity, Codex, 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 |
| Storage | LadybugDB native (fast, persistent) | LadybugDB WASM (in-memory, per session) |
| Parsing | Tree-sitter native bindings | Tree-sitter WASM |
| Privacy | Everything local, no network | Everything in-browser, no server |
Bridge mode:
gitnexus serveconnects the two — the web UI auto-detects the local server and can browse all your CLI-indexed repos without re-uploading or re-indexing.
Why a Knowledge Graph?
Tools like Cursor, Claude Code, Codex, Cline, Roo Code, and Windsurf are powerful — but they don't truly know your codebase structure. So this happens:
- AI edits
UserService.validate() - Doesn't know 47 functions depend on its return type
- Breaking changes ship
Traditional Graph RAG gives the LLM raw graph edges and hopes it explores enough. GitNexus precomputes structure at index time — clustering, tracing, scoring — so tools return complete context in one call:
flowchart TB
subgraph Traditional["Traditional Graph RAG"]
direction TB
U1["User: What depends on UserService?"]
U1 --> LLM1["LLM receives raw graph"]
LLM1 --> Q1["Query 1: Find callers"]
Q1 --> Q2["Query 2: What files?"]
Q2 --> Q3["Query 3: Filter tests?"]
Q3 --> Q4["Query 4: High-risk?"]
Q4 --> OUT1["Answer after 4+ queries"]
end
subgraph GN["GitNexus Smart Tools"]
direction TB
U2["User: What depends on UserService?"]
U2 --> TOOL["impact UserService upstream"]
TOOL --> PRECOMP["Pre-structured response:
8 callers, 3 clusters, all 90%+ confidence"]
PRECOMP --> OUT2["Complete answer, 1 query"]
end
Core innovation: Precomputed Relational Intelligence
- Reliability — the LLM can't miss context; it's already in the tool response
- Token efficiency — no 10-query chains to understand one function
- Model democratization — smaller LLMs work because the tools do the heavy lifting
What Your AI Agent Gets
17 MCP tools (15 per-repo + 2 group)
| Tool | What It Does |
|---|---|
list_repos |
Discover all indexed repositories (paginated — limit/offset) |
query |
Process-grouped hybrid search (BM25 + semantic + RRF) |
context |
360-degree symbol view — categorized refs, process participation |
impact |
Blast radius analysis with depth grouping and confidence |
trace |
Shortest directed path between two symbols (call + class-member edges) |
detect_changes |
Git-diff impact — maps changed lines to affected processes |
check |
Read-only structural checks against the indexed graph |
rename |
Multi-file coordinated rename with graph + text search |
cypher |
Raw Cypher graph queries |
route_map |
API route map — which components fetch which endpoints, and handlers |
tool_map |
MCP/RPC tool definitions — where they're defined and handled |
shape_check |
Validate API response shapes against consumers' property accesses |
api_impact |
Pre-change impact report for an API route handler |
explain |
Explain persisted taint findings (source→sink flows, --pdg indexes) |
pdg_query |
Query control/data dependence at statement level (--pdg indexes) |
group_list |
List configured repository groups |
group_sync |
Rebuild a group's Contract Registry and cross-repo links |
Per-repo tools take an optional
repoparameter (omit it when only one repo is indexed) and an optionalbranchfor indexes pinned withgitnexus analyze --branch. Omittingbranchqueries the workspace index, which follows your checked-out working tree — switching branches and re-runninggitnexus analyzeupdates it incrementally.explainandpdg_queryneed an index built withgitnexus analyze --pdg.
Resources for instant context
| Resource | Purpose |
|---|---|
gitnexus://repos |
List all indexed repositories (read this first) |
gitnexus://setup |
Setup and usage guidance for agents |
gitnexus://repo/{name}/context |
Codebase stats, staleness check, and available tools |
gitnexus://repo/{name}/clusters |
All functional clusters with cohesion scores |
gitnexus://repo/{name}/cluster/{name} |
Cluster members and details |
gitnexus://repo/{name}/processes |
All execution flows |
gitnexus://repo/{name}/process/{name} |
Full process trace with steps |
gitnexus://repo/{name}/schema |
Graph schema for Cypher queries |
gitnexus://group/{name}/contracts |
A group's extracted contracts and cross-links |
gitnexus://group/{name}/status |
Staleness of repos in a group |
2 MCP prompts for guided workflows
| Prompt | What It Does |
|---|---|
detect_impact |
Pre-commit change analysis — scope, affected processes, risk level |
generate_map |
Architecture documentation from the knowledge graph with mermaid diagrams |
Agent skills installed to .claude/skills/ and .agents/skills/ (if .agents/ exists) automatically
- Exploring — navigate unfamiliar code using the knowledge graph
- Debugging — trace bugs through call chains
- Impact Analysis — analyze blast radius before changes
- Refactoring — plan safe refactors using dependency mapping
- Guide — GitNexus tool/resource/schema reference for the agent
- CLI — run analyze/status/clean/wiki commands on request
- PDG Query — statement-level control/data dependence queries (
--pdgindex) - Taint Analysis — source→sink data-flow findings (
--pdgindex) - Plan (
/gitnexus-plan) — implementation-ready engineering plans backed by the graph and PDG slices - Work (
/gitnexus-work) — executes a plan as impact-checked,detect_changes-gated atomic commits - Review (
/gitnexus-review) — graph-backed review of a PR, branch, range, or local diff, with taint pass and per-domain expert lenses - LFG (
/gitnexus-lfg) — the full pipeline: plan → user gate → work → review
Repo-specific skills — run gitnexus analyze --skills and GitNexus detects the functional areas of your codebase (via Leiden community detection) and generates each one as a direct project skill under .claude/skills/gitnexus-area-<name>/. Each skill describes a module's key files, entry points, execution flows, and cross-area connections, and is regenerated on each --skills run to stay current.
When a repo contains an .agents/ directory, the standard and generated skills are also mirrored to .agents/skills/ (e.g. .agents/skills/gitnexus-cli/, .agents/skills/gitnexus-area-<name>/) so agents that read repo-local .agents/skills/ (like Codex) stay in sync.
Editor Setup
gitnexus setup auto-detects your editors and writes the correct global MCP config. Run it once. To configure only selected integrations, pass --coding-agent/-c with a comma-separated list, e.g. gitnexus setup -c cursor,codex.
| Editor | MCP | Skills | Hooks (auto-augment) | Support |
|---|---|---|---|---|
| Claude Code | Yes | Yes | Yes (PreToolUse + PostToolUse) | Full |
| Cursor | Yes | Yes | Yes (postToolUse, manual install) | Full |
| Antigravity (Google) | Yes | Yes | Yes (AfterTool, Gemini CLI hooks schema)¹ | Full |
| Codex | Yes | Yes | Yes (PreToolUse + PostToolUse, Codex hooks) | Full |
| OpenCode | Yes | Yes | — | MCP + Skills |
| CodeBuddy (Tencent) | Yes | Yes | — | MCP + Skills |
| Qoder (Alibaba) | Yes | Yes | — | MCP + Skills |
| Windsurf | Yes | — | — | MCP |
Claude Code and Codex get the deepest integration: MCP tools + agent skills + PreToolUse hooks that enrich searches with graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.
¹ Antigravity hooks follow the Gemini CLI hooks reference (Antigravity 2.0 is the documented successor to Gemini CLI). Augmentation runs in
AfterToolbecauseBeforeToolhas no context-injection channel in the Gemini contract — the agent sees graph context appended to the tool result viahookSpecificOutput.additionalContext. Stale-index hints land in the same channel after a successfulgit commit/merge/rebase/cherry-pick/pull. The schema may evolve if Antigravity-specific hook docs diverge from Gemini CLI's; the implementation will track those changes.
Manual MCP configuration (if you prefer not to run gitnexus setup)
Claude Code (full support — MCP + skills + hooks):
# macOS / Linux
claude mcp add gitnexus -- npx -y gitnexus@latest mcp
# Windows
claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp
Codex (full support — MCP + skills + hooks):
codex mcp add gitnexus -- npx -y gitnexus@latest mcp
Or via ~/.codex/config.toml (system scope) / .codex/config.toml (project scope):
[mcp_servers.gitnexus]
command = "npx"
args = ["-y", "gitnexus@latest", "mcp"]
Codex hooks (PreToolUse graph enrichment + PostToolUse stale-index detection in ~/.codex/hooks.json, same schema as Claude Code) need the bundled adapter script, so they are installed by gitnexus setup -c codex rather than manually.
Alternatively, install everything as a Codex plugin (MCP + skills + hooks in one step):
codex plugin marketplace add abhigyanpatwari/GitNexus
# then inside Codex: /plugins → install "GitNexus"
Codex notes: SessionStart is intentionally not registered — Codex reads AGENTS.md natively, which already carries the GitNexus context block. Newly installed hooks need a one-time approval in Codex via
/hooksbefore they run. Pick one install route (gitnexus setup -c codexor the plugin): plugin hooks load alongside~/.codex/hooks.json, so installing both can fire duplicate hooks per tool call.
Cursor (~/.cursor/mcp.json — global, works for all projects):
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
Antigravity (Google) — ~/.gemini/antigravity/mcp_config.json:
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
gitnexus setupalso merges anAfterToolentry into~/.gemini/settings.json(under the canonical Gemini CLI hooks schema) and installs skills to~/.gemini/antigravity/skills/. Existing user hooks are preserved. The hook adapter's path is rewritten at install time, so rungitnexus setuprather than hand-editing.
OpenCode (~/.config/opencode/config.json):
{
"mcp": {
"gitnexus": {
"type": "local",
"command": ["gitnexus", "mcp"]
}
}
}
CodeBuddy (Tencent) — priority chain, edit the first non-empty file that exists: ~/.codebuddy/.mcp.json (recommended) → ~/.codebuddy/mcp.json (deprecated) → ~/.codebuddy.json (legacy). CodeBuddy reads only the first existing file, so adding servers to a higher-priority file than the one currently in use would hide the servers below it. Create ~/.codebuddy/.mcp.json only if none exist:
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
Qoder (Alibaba) — ~/.qoder.json:
{
"mcpServers": {
"gitnexus": {
"command": "npx",
"args": ["-y", "gitnexus@latest", "mcp"]
}
}
}
MCP read-only mode
Set GITNEXUS_MCP_READ_ONLY=1 before starting the MCP server to expose only the proven single-repository read surface. Raw cypher, rename and group tools, group routing, and group resources are omitted from discovery and rejected before backend dispatch. Tool descriptions and generated setup/context resources are scrubbed so they do not recommend unavailable routes.
The default is unchanged when the variable is unset or 0. Any other value fails server startup rather than silently weakening the policy.
MCP repository policy
Set GITNEXUS_MCP_ALLOWED_REPOS to a comma-separated list of canonical registry names or absolute indexed paths. Entries are trimmed, resolved against the registry, and deduplicated at startup. When exactly one repository is allowed it becomes the implicit default; when several are allowed, callers must select one unless GITNEXUS_MCP_DEFAULT_REPO is also set.
The default repository must resolve to an allowed repository. Invalid, ambiguous, blank, or mismatched configuration fails startup before stdio or HTTP begins serving. The allowlist applies to tools, aliases, discovery, resources, templates, implicit resolution, and embedded HTTP; hidden repository details are not included in selection errors. Setting only GITNEXUS_MCP_DEFAULT_REPO chooses a default without restricting explicit repository selections. An allowed repository whose name is duplicated in the registry must be configured by path, and its context resource is only served for the unique name form.
MCP response budgets
The query, context, and impact tools accept an optional positive-integer maxTokens argument. It bounds the complete formatted MCP response, including hints and error text, using a deterministic four-UTF-8-bytes-per-token estimate. When truncation is required, the response ends with … and remains valid UTF-8.
Set GITNEXUS_MCP_DEFAULT_MAX_TOKENS to apply the same guardrail when callers do not send maxTokens. An explicit tool argument takes precedence. Leaving both unset preserves the existing response byte-for-byte; this is a transport guardrail, not semantic pagination or an exact model-specific tokenizer limit.
CLI Reference
Everyday commands:
gitnexus setup # Configure MCP for detected editors (one-time; -c to select)
gitnexus analyze [path] # Index a repository (or update a stale index)
gitnexus mcp # Start MCP server (stdio) — serves all indexed repos
gitnexus serve # Start local HTTP server (multi-repo) for web UI connection
gitnexus eval-server # Start lightweight evaluation HTTP tools (loopback by default)
gitnexus list # List all indexed repositories
gitnexus status # Show index status for current repo
gitnexus clean # Delete index for current repo
gitnexus wiki [path] # Generate repository wiki from knowledge graph
gitnexus uninstall # Preview removal of GitNexus MCP/skills/hooks (--force to apply)
You can also query the graph directly from the terminal — gitnexus query, context, impact, trace, cypher, detect-changes, and check mirror the MCP tools of the same names, and gitnexus doctor prints runtime platform capabilities.
Authenticated eval-server binding
gitnexus eval-server binds to 127.0.0.1 by default. Loopback bindings do not require authentication. Any non-loopback bind, including 0.0.0.0, a LAN address, or a hostname that resolves to a LAN IPv4 address, requires GITNEXUS_AUTH_TOKEN. Every endpoint then requires an exact Authorization: Bearer <token> header.
GITNEXUS_AUTH_TOKEN='replace-me' gitnexus eval-server --host 0.0.0.0
The token may be set in the shell, .env.local, or .env in the working directory. Precedence is shell > .env.local > .env. Only GITNEXUS_AUTH_TOKEN is read from those files; their other values are not added to the process environment. Keep token files uncommitted.
All analyze flags
gitnexus analyze --force # Full rebuild: re-parse + graph rebuild + FTS rebuild
gitnexus analyze --repair-fts # Fast path: rebuild/verify only FTS indexes on existing index data
gitnexus analyze --skills # Generate repo-specific skill files from detected communities
gitnexus analyze --skip-embeddings # Skip embedding generation (faster)
gitnexus analyze --embeddings [limit] # Enable embedding generation (slower, better search)
gitnexus analyze --skip-agents-md # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
gitnexus analyze --skip-skills # Skip installing standard skill files under .claude/skills/ and .agents/skills/
gitnexus analyze --skip-git # Index folders that are not Git repositories
gitnexus analyze --default-branch develop # Branch used in the generated regression-compare example (base_ref)
gitnexus analyze --verbose # Log skipped files when parsers are unavailable
gitnexus analyze --worker-timeout 60 # Increase worker idle timeout for slow parses
gitnexus analyze --workers <n> # Parse worker pool size (>=1; default: cores-1, capped at 16,
# auto-sized to the repo). 0 is rejected — there is no sequential mode.
gitnexus analyze --wal-checkpoint-threshold 67108864 # LadybugDB WAL auto-checkpoint threshold in bytes
# (default 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)
If analyze reports a worker parse timeout on a large or unusual repository, it keeps running and falls back safely. To give slow worker jobs more time, use --worker-timeout 60 or set GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000. For very large files, GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES controls the worker job byte budget.
Embeddings node limit — gitnexus analyze --embeddings generates semantic search vectors with a default 50,000-node safety cap to protect memory on large repositories:
gitnexus analyze --embeddings # default 50,000 node safety cap
gitnexus analyze --embeddings 0 # disable the cap entirely
gitnexus analyze --embeddings 100000 # custom cap
If embeddings are skipped on a large repository, the indexed graph likely exceeds the default cap — re-run with --embeddings 0 or a higher limit.
Repository groups (multi-repo / monorepo service tracking)
gitnexus group create <name> # Create a repository group
gitnexus group add <group> <groupPath> <registryName> # Add a repo. <groupPath> is a hierarchy path
# (e.g. hr/hiring/backend); <registryName> is the
# repo's name from the registry (see `gitnexus list`)
gitnexus group remove <group> <groupPath> # Remove a repo by its hierarchy path
gitnexus group list [name] # List groups, or show one group's config
gitnexus group sync <name> # Extract contracts and match across repos/services
gitnexus group contracts <name> # Inspect extracted contracts and cross-links
gitnexus group query <name> <q> # Search execution flows across all repos in a group
gitnexus group status <name> # Check staleness of repos in a group
gitnexus group impact <name> --target <symbol> --repo <groupPath> # Cross-repo blast radius
Project config (.gitnexusrc)
Commit a .gitnexusrc JSON file at the repo root to preconfigure recurring analyze options per project, instead of re-passing the same flags every run. It is read from the resolved repo root (not .gitnexus/, which is gitignored index storage). CLI flags always override .gitnexusrc.
{
// Default branch used in the generated regression-compare example (base_ref).
// Use this so a project on `develop`/`master` doesn't get "main" rewritten
// over its fix on every analyze. (Alias: "branch".)
"defaultBranch": "develop",
"skipContextFiles": true, // alias of skipAgentsMd: keep your own AGENTS.md/CLAUDE.md
"skipSkills": true, // don't install standard skill files under .claude/skills/ and .agents/skills/
"embeddings": true, // generate embeddings by default
"workerTimeout": 60,
}
A nested analyze block is also accepted (and overrides flat keys for the same option):
{ "analyze": { "defaultBranch": "develop", "skipSkills": true } }
Notes:
- The default branch is resolved as:
--default-branch>.gitnexusrcdefaultBranch/branch> auto-detectedorigin/HEAD>main. skipContextFiles/skipAiContextare aliases forskipAgentsMd— they skip theAGENTS.md/CLAUDE.mdblock only. They do not implyskipSkills.indexOnlyis the stronger option that skips all file injection.- Supported keys:
defaultBranch(branch),skipAgentsMd(skipContextFiles,skipAiContext),skipSkills,indexOnly,stats/noStats,embeddings,dropEmbeddings,name,allowDuplicateName,maxFileSize,workerTimeout,walCheckpointThreshold,workers,embeddingThreads,embeddingBatchSize,embeddingSubBatchSize,embeddingDevice. - The file is JSON only. Unknown keys and invalid values fail fast with an actionable error before analysis starts.
Environment variables
Most analyze knobs are also CLI flags (--workers, --worker-timeout, --max-file-size, --verbose). Use the env-var form when you'd otherwise repeat the same flag every run, or when invoking GitNexus from a long-running host (MCP server, eval-server, CI shell) that already manages its own environment. CLI flags take precedence over env vars; env vars take precedence over built-in defaults.
| Variable | Default | Effect | Tune when… |
|---|---|---|---|
GITNEXUS_WORKER_POOL_SIZE |
cores - 1, capped at 16 |
Parse worker pool size (must be ≥ 1). Equivalent to --workers <n>. The worker pool is the sole parse path — there is no sequential parser, so 0 is rejected with an actionable error (the pool self-heals via quarantine + respawn). |
Constrained containers (cgroup CPU limits) or CI runners with explicit quotas. To narrow down a worker crash set 1 for a single-worker pool — not 0. |
GITNEXUS_PARSE_CHUNK_CONCURRENCY |
2 |
Number of chunks whose file contents may be read into memory in parallel while the pool dispatches the current chunk. Worker dispatch itself stays serial. | Repos large enough to chunk (multi-MB total source) where disk I/O is a measurable fraction of analyze wall-clock. |
GITNEXUS_VERBOSE |
unset | When 1, enables verbose ingestion logs (skipped-file warnings, per-chunk throughput, parse-cache stats). Equivalent to --verbose. |
Debugging an analyze that "completed" but seems to have missed files; tuning --workers / chunk concurrency against observable throughput. |
GITNEXUS_AUTH_TOKEN |
unset | Bearer token required when eval-server binds beyond loopback. May also be read from .env.local or .env; shell values take precedence. |
Exposing the evaluation HTTP tools to a container, VM, or LAN. |
GITNEXUS_PROFILE_DEFERRED |
unset | When 1, emits [deferred-profile] timing/progress logs for the post-chunk deferred resolution band (imports → heritage → buildHeritageMap → legacy call resolution). Implied by GITNEXUS_VERBOSE. |
Diagnosing analyze stalls in "Resolving calls (all chunks)" on large Java/Kotlin repos (issue #1741) without the full verbose ingestion noise. |
GITNEXUS_PROFILE_DEFERRED_SLOW_MS |
3000 (verbose) / 5000 |
Per-file threshold in ms above which processCallsFromExtracted emits a slow file … log line. Parsed via Number(): accepts integers (5000), scientific notation (2.5e3), decimals (.5), and hex (0x10). Non-finite or non-positive values fall back to the default. |
Hunting a few outlier files dominating the deferred call-resolution stage; lower to surface more, raise to focus only on the worst. |
PROF_LBUG_LOAD |
unset | When 1, emits one [lbug-load prof] summary line per loadGraphToLbug call breaking the graph-DB persistence wall into stages (csv-emit / copy-nodes / copy-rels / fallback / total) plus node & edge counts. Zero-cost when unset. |
Attributing large-repo analyze wall time across CSV generation vs. LadybugDB COPY (issue #2203) — the analyze "emit" timing is the scope-resolution bucket, not this DB-write path. |
GITNEXUS_MAX_FILE_SIZE |
512 (KB) |
Walker skip threshold in KB. Hard cap is 32768 (tree-sitter buffer ceiling). Equivalent to --max-file-size <kb>. |
Indexing repos with intentionally-large source files (generated parsers, vendored bundles) that should still be parsed. |
GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS |
30000 |
Worker idle timeout in milliseconds before retry/fallback. Equivalent to --worker-timeout <seconds> × 1000. |
Slow-parsing files (large minified JS, deeply-nested TS types) that legitimately need more than 30s. |
GITNEXUS_WORKER_READY_TIMEOUT_MS |
5000 |
Startup budget in milliseconds for a parse worker to load its grammar bindings and report {type:'ready'}. Slots that miss it are treated as startup crashes. |
Slow or heavily loaded hosts where a full pool cold-starting concurrently needs more than 5s, and analyze aborts with "did not report ready within 5000ms". |
GITNEXUS_FTS_STEMMER |
porter |
Stemmer used when rebuilding BM25/FTS indexes. Use none for CJK-heavy repositories, or a language stemmer such as german, french, or spanish for matching repository comments. Re-run gitnexus analyze --repair-fts after changing it. |
Keyword search quality is poor for non-English comments or identifiers under English stemming. |
GITNEXUS_WAL_CHECKPOINT_THRESHOLD |
67108864 (64 MiB) |
LadybugDB WAL auto-checkpoint threshold in bytes. Equivalent to --wal-checkpoint-threshold <bytes>. -1 keeps LadybugDB's stock threshold (~16 MiB). Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. |
You need a larger or smaller WAL auto-checkpoint threshold for your analyze workload. |
GITNEXUS_LBUG_BUFFER_POOL_SIZE |
min(2 GiB, 80% RAM) | LadybugDB buffer-pool ceiling in bytes for every GitNexus database (analyze, MCP server, serve, group bridges). 0 restores LadybugDB's native unbounded default of 80% of system RAM; invalid values warn and fall back to the default (#2557). During analyze the pool is right-sized to the graph, scaled on non-4 KiB-page hosts by the page-size granule ratio up to min(2 GiB × pageSize/4 KiB, 80% RAM) (#2631); this env var overrides all of that as an absolute value. |
A long-lived gitnexus mcp or a big incremental analyze uses too much memory, or a huge repo's working set genuinely needs a pool larger than 2 GiB. |
GITNEXUS_LBUG_MAX_DB_SIZE |
17179869184 (16 GiB) |
Maximum size in bytes of a single LadybugDB database file — an mmap/disk-address-space ceiling, not a memory limit (it does not constrain the buffer pool). Invalid values silently fall back to the default. | Indexing a genuinely huge monorepo whose on-disk graph index approaches 16 GiB. |
GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES |
8388608 (8 MB) |
Per-job byte budget the pool will send to a worker in one postMessage. |
Very large individual files; mostly diagnostic — bumping past 8 MB risks structured-clone memory pressure. |
GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT |
3 |
Max replacement spawns per worker slot before the slot is dropped from the active rotation. Bounds respawn loops on a chronically-crashing slot. | Hosts where a flaky worker should retry more (raise) or fail-fast (lower) before the slot is dropped. |
GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS |
5 × subBatchTimeoutMs |
Total retry wall-time budget per job before quarantining. Combined with timeoutBackoffFactor, prevents exponentially-growing retries from stalling for hours. |
Slow files that legitimately need long total retry windows; lower to fail-fast on stalls. |
GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD |
max(3, poolSize) |
Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, every subsequent dispatch rejects until a fresh pool is created. | Hosts where a SIGSEGV-prone native grammar should trip the breaker sooner; CI runners that should fail loudly. |
GITNEXUS_WORKER_SHUTDOWN_DRAIN_MS |
30000 |
Max wait at pool shutdown for a retired worker still inside native code. The worker is terminated at its next JS-safe point instead of mid-native-call (which aborts the whole process with Napi::Error, #2432); on expiry it is left running, unref'd, and terminated when it surfaces. |
Shutdown latency matters more than draining a wedged worker (lower), or a legitimately-slow native grammar needs longer to surface (raise). |
GITNEXUS_CPP_CAPTURE_BUDGET_MS |
20000 |
Per-file wall-clock budget for C++ capture extraction. On breach the file keeps the captures accumulated so far and logs a warning — the worker returns to JS instead of stalling in native-heavy loops (#2432). 0 expires immediately. |
Pathological generated C++ that still exceeds the budget after the indexed lookups; raise for completeness, lower to fail-fast. |
GITNEXUS_CHUNK_BYTE_BUDGET |
2097152 (2 MB) |
Chunk boundary used for cache-key composition and dispatch. Smaller = finer-grained cache hits but more dispatch overhead. | Tuning incremental-analyze cache behavior on monorepos. |
GITNEXUS_NO_GITIGNORE |
unset | When set, skips .gitignore parsing. .gitnexusignore is still honored. |
Indexing a repo whose .gitignore excludes files you actually want indexed (e.g., generated code committed for cross-repo lookup). |
GITNEXUS_SKIP_OPTIONAL_GRAMMARS |
unset | When =1 strictly, skips the vendored grammar materialize for tree-sitter-dart, tree-sitter-proto, tree-sitter-swift, and tree-sitter-kotlin at install time (and the Dart/Proto source builds). Those four won't be parsed; the install still succeeds. |
Installing on a host without a C++ toolchain or where the vendored prebuilds don't match; willing to skip Dart/Proto/Swift/Kotlin parsing. |
GITNEXUS_MCP_READ_ONLY |
unset | Set to 1 to expose only proven single-repository read tools and resources; 0 disables the policy and any other value fails startup. |
The MCP server runs in an environment where graph mutation, raw Cypher, and cross-repository group routing must be unavailable. |
GITNEXUS_MCP_ALLOWED_REPOS |
unset | Comma-separated allowlist of canonical indexed repository names or absolute paths. Invalid, ambiguous, or blank entries fail startup. | One MCP process must expose only a bounded subset of the repositories in the global registry. |
GITNEXUS_MCP_DEFAULT_REPO |
unset | Canonical indexed repository name or absolute path used when a tool or resource omits its repository. Must belong to the allowlist when one is set. | Several repositories are available but unqualified MCP calls should resolve deterministically. |
GITNEXUS_MCP_DEFAULT_MAX_TOKENS |
unset | Default positive-integer response budget for MCP query, context, and impact, estimated at four UTF-8 bytes per token. Explicit maxTokens wins. |
Long MCP responses consume too much model context and callers cannot reliably add a per-request budget. |
gitnexus uninstall
gitnexus uninstall reverses gitnexus setup — it removes the GitNexus MCP entries, hooks, and skill directories it added to each detected editor. Skill directories are identified by bundled gitnexus skill name (e.g. gitnexus-cli/), so if you customized files inside an installed skill directory, back them up first. It is a dry-run preview by default and prints the exact paths it would remove; pass --force to apply. Per-repo indexes (gitnexus clean --all) and the global npm package (npm uninstall -g gitnexus) are left for you to remove.
Publishing to understand-quickly (opt-in)
looptech-ai/understand-quickly is a public registry of code-knowledge graphs that lists gitnexus@1 as a first-class format. After registering your repo once (npx @understand-quickly/cli add or the wizard), gitnexus publish fires a single repository_dispatch event so the registry resyncs your entry on demand instead of waiting for the nightly job.
It is opt-in and a no-op without UNDERSTAND_QUICKLY_TOKEN — a fine-grained GitHub PAT with Repository dispatches: write on the registry repo. Nothing else happens; no graph file is uploaded. See the protocol spec for the full contract.
How It Works
GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:
- Structure — walks the file tree and maps folder/file relationships
- Parsing — extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
- Resolution — resolves imports, function calls, heritage, constructor inference, and
self/thisreceiver types across files with language-aware logic - Clustering — groups related symbols into functional communities
- Processes — traces execution flows from entry points through call chains
- 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++ | — | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
| Dart | ✓ | — | ✓ | ✓ | ✓ | ✓ | — | ✓ | ✓ |
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
Control flow (CFG, opt-in --pdg) — per-function control-flow graphs (BasicBlock nodes + CFG edges) feeding the PDG/taint substrate, currently TypeScript & JavaScript (#2081 M1); other languages planned. Off by default.
Multi-Repo Architecture
GitNexus uses a global registry so one MCP server can serve multiple indexed repos. No per-project MCP config needed — set it up once and it works everywhere.
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.
Architecture diagram
flowchart TD
subgraph CLI [CLI Commands]
Setup["gitnexus setup"]
Analyze["gitnexus analyze"]
Clean["gitnexus clean"]
List["gitnexus list"]
end
subgraph Registry ["~/.gitnexus/"]
RegFile["registry.json"]
end
subgraph Repos [Project Repos]
RepoA[".gitnexus/ in repo A"]
RepoB[".gitnexus/ in repo B"]
end
subgraph MCP [MCP Server]
Server["server.ts"]
Backend["LocalBackend"]
Pool["Connection Pool"]
ConnA["LadybugDB conn A"]
ConnB["LadybugDB conn B"]
end
Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
Analyze -->|"registers repo"| RegFile
Analyze -->|"stores index"| RepoA
Clean -->|"unregisters repo"| RegFile
List -->|"reads"| RegFile
Server -->|"reads registry"| RegFile
Server --> Backend
Backend --> Pool
Pool -->|"lazy open"| ConnA
Pool -->|"lazy open"| ConnB
ConnA -->|"queries"| RepoA
ConnB -->|"queries"| RepoB
Tool Examples
Impact Analysis
impact({target: "UserService", direction: "upstream", minConfidence: 0.8})
TARGET: Class UserService (src/services/user.ts)
UPSTREAM (what depends on this):
Depth 1 (WILL BREAK):
handleLogin [CALLS 90%] -> src/api/auth.ts:45
handleRegister [CALLS 90%] -> src/api/auth.ts:78
UserController [CALLS 85%] -> src/controllers/user.ts:12
Depth 2 (LIKELY AFFECTED):
authRouter [IMPORTS] -> src/routes/auth.ts
Options: maxDepth, minConfidence, relationTypes (CALLS, IMPORTS, EXTENDS, IMPLEMENTS), includeTests, limit (max symbols per depth, default 100), offset (pagination start per depth), summaryOnly (counts and risk only, omits symbol list)
Disambiguation — when several symbols share the target name, impact returns a ranked ambiguous candidate list instead of guessing. Narrow it with target_uid (exact, zero-ambiguity), file_path, or kind (Function, Class, Method, …). From the CLI these are --uid, --file, and --kind, matching gitnexus context:
gitnexus impact get_embeddings # → ambiguous: lists ranked candidates
gitnexus impact get_embeddings --file src/embed.py # → resolves to the one in that file
gitnexus impact get_embeddings --uid "Function:src/embed.py:get_embeddings" # exact
More examples: search · context · detect_changes · rename · Cypher
Process-Grouped Search
query({search_query: "authentication middleware"})
processes:
- summary: "LoginFlow"
priority: 0.042
symbol_count: 4
process_type: cross_community
step_count: 7
process_symbols:
- name: validateUser
type: Function
filePath: src/auth/validate.ts
process_id: proc_login
step_index: 2
definitions:
- name: AuthConfig
type: Interface
filePath: src/types/auth.ts
Context (360-degree Symbol View)
context({name: "validateUser"})
symbol:
uid: "Function:validateUser"
kind: Function
filePath: src/auth/validate.ts
startLine: 15
incoming:
calls: [handleLogin, handleRegister, UserController]
imports: [authRouter]
outgoing:
calls: [checkPassword, createSession]
processes:
- name: LoginFlow (step 2/7)
- name: RegistrationFlow (step 3/5)
Detect Changes (Pre-Commit)
detect_changes({scope: "all"})
summary:
changed_count: 12
affected_count: 3
changed_files: 4
risk_level: medium
changed_symbols: [validateUser, AuthService, ...]
affected_processes: [LoginFlow, RegistrationFlow, ...]
Rename (Multi-File)
rename({symbol_name: "validateUser", new_name: "verifyUser", dry_run: true})
status: success
files_affected: 5
total_edits: 8
graph_edits: 6 (high confidence)
text_search_edits: 2 (review carefully)
changes: [...]
Cypher Queries
-- Find what calls auth functions with high confidence
MATCH (c:Community {heuristicLabel: 'Authentication'})<-[:CodeRelation {type: 'MEMBER_OF'}]-(fn)
MATCH (caller)-[r:CodeRelation {type: 'CALLS'}]->(fn)
WHERE r.confidence > 0.8
RETURN caller.name, fn.name, r.confidence
ORDER BY r.confidence DESC
Wiki Generation
Generate LLM-powered documentation from your knowledge graph:
# Requires an LLM API key (OPENAI_API_KEY, etc.)
gitnexus wiki
# Use a custom model or provider (default model: minimax/minimax-m2.5)
gitnexus wiki --model gpt-4o
gitnexus wiki --base-url https://api.anthropic.com/v1
# Force full regeneration
gitnexus wiki --force
# Increase the timeout or retries for large codebases or slow LLM providers
gitnexus wiki --timeout <seconds> # LLM request timeout in seconds (default: disabled)
gitnexus wiki --retries <n> # Max LLM retry attempts per request (default: 3)
# Allow a specific LAN/self-hosted HTTP LLM host (HTTPS is preferred for remote endpoints)
gitnexus wiki --base-url http://llama-box.local:8080/v1 --allow-insecure-connection llama-box.local
# Or set a comma-separated host allowlist:
GITNEXUS_ALLOW_INSECURE_CONNECTION=llama-box.local,192.168.1.23
# Change the output language
gitnexus wiki --lang <lang> # e.g. english, chinese, spanish, japanese
For safety, http:// LLM base URLs are allowed by default only for loopback hosts (localhost, 127.0.0.1, ::1). --allow-insecure-connection and GITNEXUS_ALLOW_INSECURE_CONNECTION accept exact hostnames or IP addresses only; do not include schemes, ports, paths, credentials, or wildcards.
The wiki generator reads the indexed graph structure, groups files into modules via LLM, generates per-module documentation pages, and creates an overview page — all with cross-references to the knowledge graph.
Web UI (browser-based)
A client-side graph explorer and AI chat — your code never leaves your machine.
Try it now: gitnexus.vercel.app — run npx gitnexus@latest serve locally and the page auto-connects to your local backend.
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.
Local Backend Mode: run gitnexus serve and open the web UI — it auto-detects the server and shows all your indexed repos, with full AI chat support. No re-upload, no re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.
Run the frontend locally
git clone https://github.com/abhigyanpatwari/gitnexus.git
cd gitnexus/gitnexus-shared && npm install && npm run build
cd ../gitnexus-web && npm install
npm run dev
# Then in another terminal, start the backend the frontend connects to:
npx gitnexus@latest serve
Docker
docker compose up -d
This starts the server on http://localhost:4747 and the web UI on http://localhost:4173. The UI auto-detects the server because the browser runs on the host and reaches the container via the mapped port.
The official setup ships two signed images, published identically to GitHub Container Registry (GHCR) and Docker Hub — same build, same digest, same Cosign signature:
| Purpose | GHCR (default in docker-compose.yaml) |
Docker Hub mirror |
|---|---|---|
CLI / gitnexus serve backend (HTTP API on port 4747, MCP, indexer) |
ghcr.io/abhigyanpatwari/gitnexus:latest |
akonlabs/gitnexus:latest |
Static web UI (port 4173) |
ghcr.io/abhigyanpatwari/gitnexus-web:latest |
akonlabs/gitnexus-web:latest |
A named volume (gitnexus-data) persists the global registry, indexes, and cloned repos at /data/gitnexus inside the server container. To make repos on your host machine indexable, set WORKSPACE_DIR before bringing the stack up:
WORKSPACE_DIR=$HOME/code docker compose up -d
# Inside the server container the directory is mounted read-only at /workspace.
docker compose exec gitnexus-server gitnexus index /workspace/my-repo
Heads-up — image rename. Earlier releases published the web UI under
ghcr.io/abhigyanpatwari/gitnexus. That slug now hosts the CLI/server image and the UI moved toghcr.io/abhigyanpatwari/gitnexus-web. Previous tags remain pullable, but new versions are only published under the new slugs — update yourdocker run/ compose files (or just adopt the bundled compose).
Direct docker run & env file
# Server
docker run --rm -d \
--name gitnexus-server \
-p 4747:4747 \
-v gitnexus-data:/data/gitnexus \
ghcr.io/abhigyanpatwari/gitnexus:latest
# Web UI
docker run --rm -d \
--name gitnexus-web \
-p 4173:4173 \
ghcr.io/abhigyanpatwari/gitnexus-web:latest
Optional env file (override image tags, container names, ports, workspace dir):
cp .env.example .env
docker compose --env-file .env up -d
Files:
- Dockerfile.web — builds
gitnexus-sharedandgitnexus-web, then serves the production frontend. - Dockerfile.cli — builds the CLI/server (with its native deps) and runs
gitnexus serve --host 0.0.0.0. - docker-compose.yaml — starts both signed images side by side.
- .env.example — overrides for image names, container names, ports, and the workspace mount.
Versioning & supply-chain protection (Cosign signatures, provenance, Kubernetes admission policy)
The Docker images are version-locked to the npm package:
- Stable images are only published from
vX.Y.Zgit tags (viadocker.ymltriggered directly by the tag push), and the workflow refuses to build unless the tag exactly matchesgitnexus/package.json's version. Soghcr.io/abhigyanpatwari/gitnexus:1.6.2(and its Docker Hub mirrorakonlabs/gitnexus:1.6.2) is byte-for-byte the same release asnpm install gitnexus@1.6.2— no drift, no floating builds frommain. Both registries receive the same digest from a single build step, so you can pull from either and the signature verifies identically. - Release-candidate images (e.g.
:1.7.0-rc.1) are published alongside each RC npm release. They are built bypublish.ymlcallingdocker.ymlas a reusable workflow after the RC tag is created and pushed. :latestis auto-promoted only from non-prerelease tags by the Docker metadata action, so it always points at a real, npm-published version.
Both images are signed with Cosign keyless signing using the workflow's GitHub OIDC identity, and shipped with build provenance and SBOM attestations. This is your protection against supply-chain attacks: even if an attacker republishes a same-named image elsewhere (or somehow pushes to a typo-squatted registry), they cannot forge a Cosign signature tied to abhigyanpatwari/GitNexus's docker.yml. Always verify before pulling into sensitive environments.
Stable releases — signed from the v* tag ref:
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
--certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
--certificate-oidc-issuer https://token.actions.githubusercontent.com
# Same signature verifies the Docker Hub mirror (identical digest):
cosign verify docker.io/akonlabs/gitnexus:1.6.2 \
--certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
--certificate-oidc-issuer https://token.actions.githubusercontent.com
The regex pins the certificate identity to this repo's docker.yml workflow run from a v* tag — rejecting unsigned images, images signed by other workflows, and images signed from unprotected refs. It is identical for both registries because both sets of tags were signed at the same digest in one workflow run.
Release candidates — signed from refs/heads/main (the caller's ref when publish.yml invokes docker.yml as a reusable workflow):
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.7.0-rc.1 \
--certificate-identity 'https://github.com/abhigyanpatwari/GitNexus/.github/workflows/docker.yml@refs/heads/main' \
--certificate-oidc-issuer https://token.actions.githubusercontent.com
You can also inspect the build provenance and SBOM:
cosign download attestation ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
--predicate-type https://slsa.dev/provenance/v1
Kubernetes: enforce signatures at admission. Ship the bundled ClusterImagePolicy so the Sigstore policy-controller rejects any GitNexus pod whose image is not signed by this repo's docker.yml running from a vX.Y.Z tag — the same identity the cosign verify snippet above pins.
# 1. Install the controller (one-time, cluster-wide)
helm repo add sigstore https://sigstore.github.io/helm-charts && helm repo update
helm install policy-controller -n cosign-system --create-namespace \
sigstore/policy-controller
# 2. Opt your namespace in
kubectl label namespace <your-ns> policy.sigstore.dev/include=true
# 3. Apply the policy
kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml
After this, attempting to deploy an unsigned image — or one signed by anything other than abhigyanpatwari/GitNexus's docker.yml at a v* tag — fails the admission webhook before a pod is ever created. This turns the verifiable signature into an enforced policy, which is the supply-chain control most clusters actually need.
Enterprise
GitNexus is available as an enterprise offering — fully managed SaaS or self-hosted deployment. Commercial use of the OSS version is also available with proper licensing.
Enterprise includes:
- PR Review — automated blast radius analysis on pull requests
- Auto-updating Code Wiki — always up-to-date documentation (Code Wiki is also available in OSS)
- Auto-reindexing — knowledge graph stays fresh automatically
- Multi-repo support — unified graph across repositories
- OCaml support — additional language coverage
- Priority feature/language support — request new languages or features
Upcoming: auto regression forensics · end-to-end test generation
👉 Learn more at akonlabs.com — for commercial licensing or enterprise inquiries, ping us on Discord or email founders@akonlabs.com
Community Integrations
Built by the community — not officially maintained, but worth checking out.
| Project | Author | Description |
|---|---|---|
| pi-gitnexus | @tintinweb | GitNexus plugin for pi — pi install npm:pi-gitnexus |
| gitnexus-stable-ops | @ShunsukeHayashi | Stable ops & deployment workflows (Miyabi ecosystem) |
| KiloCode MCP workflow | @oktanishq | Guide to connect GitNexus MCP to Kilo Code and verify tools. |
Have a project built on GitNexus? Open a PR to add it here!
Roadmap
Actively building:
- LLM Cluster Enrichment — semantic cluster names via LLM API
- AST Decorator Detection — parse @Controller, @Get, etc.
- Incremental Indexing — only re-index changed files
Recently completed:
- Constructor-Inferred Type Resolution,
self/thisReceiver Mapping - Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
- Process-Grouped Search, 360-Degree Context, Claude Code Hooks
- Multi-Repo MCP, Zero-Config Setup, 14 Language Support
- Community Detection, Process Detection, Confidence Scoring
- Hybrid Search, Vector Index
Development
- ARCHITECTURE.md — packages, index → graph → MCP flow, where to change code
- RUNBOOK.md — analyze, embeddings, stale index, MCP recovery, CI snippets
- GUARDRAILS.md — safety rules and operational "Signs" for contributors and agents
- CONTRIBUTING.md — license, setup, commits, and pull requests
- TESTING.md — test commands for
gitnexusandgitnexus-web
Tech Stack
| Layer | CLI | Web |
|---|---|---|
| Runtime | Node.js (native) | Browser (WASM) |
| Parsing | Tree-sitter native bindings | Tree-sitter WASM |
| Database | LadybugDB native | LadybugDB 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 |
| Visualization | — | Sigma.js + Graphology (WebGL) |
| Frontend | — | React 18, TypeScript, Vite, Tailwind v4 |
| Clustering | Graphology | Graphology |
| Concurrency | Worker threads + async | Web Workers + Comlink |
Security & Privacy
- CLI: everything runs locally on your machine. No network calls. Index stored in
.gitnexus/(gitignored). Global registry at~/.gitnexus/stores only paths and metadata. - Web: everything runs in your browser. No code uploaded to any server. API keys stored in localStorage only.
- Open source — audit the code yourself.
Star History
Acknowledgments
- Tree-sitter — AST parsing
- LadybugDB — embedded graph database with vector support (formerly KuzuDB)
- Sigma.js — WebGL graph rendering
- transformers.js — browser ML
- Graphology — graph data structures
- MCP — Model Context Protocol