docs(ai-context): address PR #1508 review findings on keep-marker path

- Clarify that noStats affects generated template only, not keep-section stats updates
- Fix stats-line regex comment to match behavior (no end anchor; trailing suffix kept)
- Assert '. MCP tools.' survives stats replacement in preserve-custom-section test
- Document LF normalization when rewriting CRLF seed in keep-marker CRLF test

Co-authored-by: Cursor <cursoragent@cursor.com>

gitnexus/src/cli/ai-context.ts

@@ -199,7 +199,9 @@ async function fileExists(filePath: string): Promise<boolean> {
 async function upsertGitNexusSection(
   filePath: string,
   content: string,
-): Promise<'created' | 'updated' | 'appended'> {
+  projectName: string,
+  stats: RepoStats,
+): Promise<'created' | 'updated' | 'appended' | 'preserved'> {
   const exists = await fileExists(filePath);
 
   if (!exists) {
@@ -223,7 +225,50 @@ async function upsertGitNexusSection(
   );
 
   if (startIdx !== -1 && endIdx !== -1 && endIdx > startIdx) {
-    // Replace existing section
+    const existingSection = existingContent.substring(
+      startIdx,
+      endIdx + GITNEXUS_END_MARKER.length,
+    );
+
+    // If the existing section contains <!-- gitnexus:keep -->, preserve the user's
+    // custom layout and only update the stats line (node/edge/flow counts).
+    // This lets teams trim the verbose default template to a lean format without
+    // having it overwritten on every `gitnexus analyze`.
+    //
+    // Note: the keep-marker check operates on `existingSection` (the substring
+    // between valid section markers identified by findSectionMarkerIndex), so
+    // a keep marker in user prose OUTSIDE the GitNexus block has no effect.
+    if (existingSection.includes('<!-- gitnexus:keep -->')) {
+      // Build the new stats line from the caller-provided values directly.
+      // We do NOT re-extract from `content` because:
+      //   (a) first-bold extraction is fragile if the template evolves
+      //   (b) the parenthesized-text fallback can match unrelated tuples
+      //       like `({target: "symbolName", direction: "upstream"})`
+      //       when noStats is set
+      // Passing projectName + stats explicitly makes the contract obvious.
+      // noStats controls template generation, not keep-section stat updates — the user opted into a stats line by keeping it.
+      const newStatsInner = `${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows`;
+      const statsLine = `Indexed as **${projectName}** (${newStatsInner})`;
+
+      // Match either canonical phrasing at line start (`^` with `m` flag) so we
+      // cannot replace prose embedded mid-paragraph. Deliberately no `$`: text
+      // after the closing `)` on the same line (e.g. ". MCP tools.") stays intact.
+      const statsPattern = /^(?:Indexed as|indexed by GitNexus as) \*\*[^*]+\*\* \([^)]+\)/m;
+
+      if (statsPattern.test(existingSection)) {
+        const updatedSection = existingSection.replace(statsPattern, statsLine);
+        const before = existingContent.substring(0, startIdx);
+        const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
+        await fs.writeFile(filePath, (before + updatedSection + after).trim() + '\n', 'utf-8');
+        return 'updated';
+      }
+      // Keep marker present but no stats line matched. Section is preserved
+      // unchanged on disk; return a distinct status so callers/CLI output
+      // don't mis-report this as 'updated' (which would imply a write).
+      return 'preserved';
+    }
+
+    // No keep marker — replace existing section with full verbose content
     const before = existingContent.substring(0, startIdx);
     const after = existingContent.substring(endIdx + GITNEXUS_END_MARKER.length);
     const newContent = before + content + after;
@@ -344,12 +389,12 @@ export async function generateAIContextFiles(
   if (!options?.skipAgentsMd) {
     // Create AGENTS.md (standard for Cursor, Windsurf, OpenCode, Cline, etc.)
     const agentsPath = path.join(repoPath, 'AGENTS.md');
-    const agentsResult = await upsertGitNexusSection(agentsPath, content);
+    const agentsResult = await upsertGitNexusSection(agentsPath, content, projectName, stats);
     createdFiles.push(`AGENTS.md (${agentsResult})`);
 
     // Create CLAUDE.md (for Claude Code)
     const claudePath = path.join(repoPath, 'CLAUDE.md');
-    const claudeResult = await upsertGitNexusSection(claudePath, content);
+    const claudeResult = await upsertGitNexusSection(claudePath, content, projectName, stats);
     createdFiles.push(`CLAUDE.md (${claudeResult})`);
   } else {
     createdFiles.push('AGENTS.md (skipped via --skip-agents-md)');

gitnexus/test/unit/ai-context.test.ts

@@ -123,9 +123,81 @@ describe('generateAIContextFiles', () => {
     expect(starts).toBe(1);
   });
 
+  it('preserves custom section when gitnexus:keep is present', async () => {
+    const claudeMdPath = path.join(tmpDir, 'CLAUDE.md');
+
+    // Write a custom lean section with keep marker
+    const customContent = `# My Project
+
+Some project docs here.
+
+<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+# GitNexus — Code Knowledge Graph
+
+Indexed as **TestProject** (50 symbols, 100 relationships, 5 execution flows). MCP tools.
+
+| Tool | Use for |
+|------|---------|
+| query | Find flows |
+
+Resources: gitnexus://repo/TestProject/context
+<!-- gitnexus:end -->
+`;
+    await fs.writeFile(claudeMdPath, customContent, 'utf-8');
+
+    // Run analyze with new stats — should only update the stats line
+    const stats = { nodes: 999, edges: 1234, processes: 42 };
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+
+    const result = await fs.readFile(claudeMdPath, 'utf-8');
+
+    // Stats should be updated
+    expect(result).toContain('999 symbols');
+    expect(result).toContain('1234 relationships');
+    expect(result).toContain('42 execution flows');
+    expect(result).toContain('. MCP tools.');
+
+    // Custom layout should be preserved (not replaced with verbose template)
+    expect(result).toContain('<!-- gitnexus:keep -->');
+    expect(result).toContain('Code Knowledge Graph');
+    expect(result).toContain('| query | Find flows |');
+
+    // Verbose template sections should NOT be present
+    expect(result).not.toContain('## Always Do');
+    expect(result).not.toContain('## Never Do');
+    expect(result).not.toContain('## When Debugging');
+
+    // Non-GitNexus content should be preserved
+    expect(result).toContain('# My Project');
+    expect(result).toContain('Some project docs here.');
+  });
+
+  it('replaces section when no keep marker is present', async () => {
+    const agentsPath = path.join(tmpDir, 'AGENTS.md');
+
+    // Write a section WITHOUT keep marker
+    const content = `<!-- gitnexus:start -->
+# GitNexus — Code Intelligence
+
+Old content here.
+<!-- gitnexus:end -->
+`;
+    await fs.writeFile(agentsPath, content, 'utf-8');
+
+    const stats = { nodes: 100, edges: 200, processes: 10 };
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+
+    const result = await fs.readFile(agentsPath, 'utf-8');
+
+    // Should have the full verbose template
+    expect(result).toContain('## Always Do');
+    expect(result).not.toContain('Old content here');
+  });
+
   it('installs skills files', async () => {
     const stats = { nodes: 10 };
-    const result = await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
+    await generateAIContextFiles(tmpDir, storagePath, 'TestProject', stats);
 
     // Should have installed skill files
     const skillsDir = path.join(tmpDir, '.claude', 'skills', 'gitnexus');
@@ -371,4 +443,240 @@ describe('generateAIContextFiles', () => {
       await fs.rm(crlfDir, { recursive: true, force: true });
     }
   });
+
+  // ──────────────────────────────────────────────────────────────────
+  // Keep-marker edge cases (added to address PR #1508 review findings)
+  // ──────────────────────────────────────────────────────────────────
+
+  it('keep marker OUTSIDE the GitNexus section has no effect (#1508 review F5)', async () => {
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-scope-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      // Keep marker appears in user prose BEFORE the GitNexus section.
+      // The keep-path must NOT be triggered — full template replacement
+      // is the correct behavior here, because the marker is not inside
+      // the generated block.
+      const fileWithOutOfBandMarker = `# My Project
+
+A note about <!-- gitnexus:keep --> markers: they only apply inside the
+GitNexus block below, not in prose like this.
+
+<!-- gitnexus:start -->
+Old verbose stub here.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(claudePath, fileWithOutOfBandMarker, 'utf-8');
+
+      const stats = { nodes: 50, edges: 100, processes: 5 };
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), 'TestProject', stats);
+
+      const result = await fs.readFile(claudePath, 'utf-8');
+      // Section MUST have been fully replaced — keep marker outside section ignored
+      expect(result).toContain('## Always Do');
+      expect(result).not.toContain('Old verbose stub here.');
+      // User's prose with the marker reference is preserved untouched
+      expect(result).toContain('A note about <!-- gitnexus:keep --> markers');
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it('AGENTS.md keep path preserves custom layout (#1508 review F5)', async () => {
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-agents-'));
+    try {
+      const agentsPath = path.join(dir, 'AGENTS.md');
+      const customAgents = `# AGENTS instructions
+
+Project-specific agent guidance.
+
+<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+# GitNexus context for AGENTS
+
+Indexed as **AgentsTest** (10 symbols, 20 relationships, 1 execution flows).
+
+Use 'query' for finding flows, 'context' for symbol details.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(agentsPath, customAgents, 'utf-8');
+
+      const stats = { nodes: 777, edges: 888, processes: 9 };
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), 'AgentsTest', stats);
+
+      const result = await fs.readFile(agentsPath, 'utf-8');
+      // Stats updated
+      expect(result).toContain('777 symbols');
+      expect(result).toContain('888 relationships');
+      expect(result).toContain('9 execution flows');
+      // Custom layout preserved
+      expect(result).toContain('# GitNexus context for AGENTS');
+      expect(result).toContain("Use 'query' for finding flows");
+      // Verbose template NOT injected
+      expect(result).not.toContain('## Always Do');
+      // Non-GitNexus content preserved
+      expect(result).toContain('# AGENTS instructions');
+      expect(result).toContain('Project-specific agent guidance.');
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it('idempotent: second run with keep marker produces byte-identical output (#1508 review F5)', async () => {
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-idem-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      const seed = `# Project
+
+<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+Indexed as **Idem** (1 symbols, 2 relationships, 3 execution flows). Custom.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(claudePath, seed, 'utf-8');
+
+      const stats = { nodes: 99, edges: 100, processes: 7 };
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), 'Idem', stats);
+      const afterFirst = await fs.readFile(claudePath, 'utf-8');
+
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), 'Idem', stats);
+      const afterSecond = await fs.readFile(claudePath, 'utf-8');
+
+      expect(afterSecond).toBe(afterFirst);
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it('CRLF file with keep marker: stats line updates without corrupting content (#1508 review F5)', async () => {
+    // upsertGitNexusSection writes with .trim() + '\n', so the saved file uses LF
+    // line endings throughout — CRLF in the seed input is not preserved.
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-crlf-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      const crlfContent =
+        '# Project\r\n' +
+        '\r\n' +
+        '<!-- gitnexus:start -->\r\n' +
+        '<!-- gitnexus:keep -->\r\n' +
+        'Indexed as **CRLFTest** (5 symbols, 6 relationships, 7 execution flows). Custom CRLF.\r\n' +
+        '<!-- gitnexus:end -->\r\n';
+      await fs.writeFile(claudePath, crlfContent, 'utf-8');
+
+      const stats = { nodes: 50, edges: 60, processes: 7 };
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), 'CRLFTest', stats);
+
+      const result = await fs.readFile(claudePath, 'utf-8');
+      // Stats updated correctly
+      expect(result).toContain('50 symbols');
+      expect(result).toContain('60 relationships');
+      // Custom prose preserved
+      expect(result).toContain('Custom CRLF');
+      // No verbose template injected
+      expect(result).not.toContain('## Always Do');
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it('noStats + keep marker: stats line update is NOT corrupted by Always-Do tuple text (#1508 review F3)', async () => {
+    // Regression guard: with the old fallback regex `\(([^)]+)\)`, when
+    // noStats=true suppressed the canonical stats line from generated
+    // content, the fallback matched the FIRST parenthesized text in the
+    // template, which was `({target: "symbolName", direction: "upstream"})`
+    // from the Always Do bullet — silently writing that as the stats line.
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-nostats-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      const seed = `<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+Indexed as **NoStatsTest** (1 symbols, 1 relationships, 1 execution flows). Custom.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(claudePath, seed, 'utf-8');
+
+      const stats = { nodes: 42, edges: 84, processes: 3 };
+      await generateAIContextFiles(
+        dir,
+        path.join(dir, '.gitnexus'),
+        'NoStatsTest',
+        stats,
+        undefined,
+        { noStats: true },
+      );
+
+      const result = await fs.readFile(claudePath, 'utf-8');
+      // Stats line MUST NOT have been corrupted with the Always-Do tuple text
+      expect(result).not.toMatch(/\(\{target:/);
+      expect(result).not.toMatch(/direction:\s*"upstream"/);
+      // Stats line should reflect a sensible numeric update (passed stats)
+      expect(result).toContain('42 symbols');
+      // Custom prose still preserved
+      expect(result).toContain('Custom.');
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it("returns 'preserved' (not 'updated') when keep marker is present but no stats line matches (#1508 review F1)", async () => {
+    // Regression guard for the misleading-return-value bug: previously the
+    // function returned 'updated' without writing when the keep-section had
+    // no recognizable stats line, causing CLI output to claim files were
+    // updated when they were not.
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-noline-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      // Custom keep-section with NO "Indexed as ..." or "indexed by GitNexus as ..." line
+      const seed = `# Project
+
+<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+# GitNexus block (custom, no stats line)
+
+This block intentionally omits the standard stats line.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(claudePath, seed, 'utf-8');
+
+      const stats = { nodes: 100, edges: 200, processes: 10 };
+      const result = await generateAIContextFiles(
+        dir,
+        path.join(dir, '.gitnexus'),
+        'NoLineTest',
+        stats,
+      );
+
+      // The result manifest should reflect 'preserved', not 'updated'
+      expect(result.files).toContain('CLAUDE.md (preserved)');
+      // File on disk is unchanged
+      const onDisk = await fs.readFile(claudePath, 'utf-8');
+      expect(onDisk).toBe(seed);
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
+
+  it('project name with markdown-sensitive punctuation lands intact in stats line (#1508 review F5)', async () => {
+    const dir = await fs.mkdtemp(path.join(os.tmpdir(), 'gn-keep-punct-'));
+    try {
+      const claudePath = path.join(dir, 'CLAUDE.md');
+      const seed = `<!-- gitnexus:start -->
+<!-- gitnexus:keep -->
+Indexed as **placeholder** (1 symbols, 1 relationships, 1 execution flows). Custom.
+<!-- gitnexus:end -->
+`;
+      await fs.writeFile(claudePath, seed, 'utf-8');
+
+      // Name with hyphens, dot, and slash — exactly what dp-web4/some-repo
+      // style names look like
+      const trickyName = 'dp-web4/some-repo.v2';
+      const stats = { nodes: 5, edges: 10, processes: 1 };
+      await generateAIContextFiles(dir, path.join(dir, '.gitnexus'), trickyName, stats);
+
+      const result = await fs.readFile(claudePath, 'utf-8');
+      // The full name appears in the bold of the stats line, intact
+      expect(result).toContain(`Indexed as **${trickyName}** (5 symbols`);
+    } finally {
+      await fs.rm(dir, { recursive: true, force: true });
+    }
+  });
 });