gitnexus 1.3.9 → 1.3.11

package/README.md

@@ -1,194 +1,194 @@
-# GitNexus
-
-**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**, **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/)
-
----
-
-## Why?
-
-AI coding tools don't understand your codebase structure. They edit a function without knowing 47 other functions depend on it. GitNexus fixes this by **precomputing every dependency, call chain, and relationship** into a queryable graph.
-
-**Three commands to give your AI agent full codebase awareness.**
-
-## Quick Start
-
-```bash
-# Index your repo (run from repo root)
-npx gitnexus analyze
-```
-
-That's it. This indexes the codebase, installs agent skills, registers Claude Code hooks, and creates `AGENTS.md` / `CLAUDE.md` context files — all in one command.
-
-To configure MCP for your editor, run `npx gitnexus setup` once — or set it up manually below.
-
-`gitnexus setup` auto-detects your editors and writes the correct global MCP config. You only need to run it once.
-
-### Editor Support
-
-| Editor | MCP | Skills | Hooks (auto-augment) | Support |
-|--------|-----|--------|---------------------|---------|
-| **Claude Code** | Yes | Yes | Yes (PreToolUse) | **Full** |
-| **Cursor** | Yes | Yes | — | MCP + Skills |
-| **Windsurf** | Yes | — | — | MCP |
-| **OpenCode** | Yes | Yes | — | MCP + Skills |
-
-> **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
-
-| Agent | Install | Source |
-|-------|---------|--------|
-| [pi](https://pi.dev) | `pi install npm:pi-gitnexus` | [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus) |
-
-## MCP Setup (manual)
-
-If you prefer to configure manually instead of using `gitnexus setup`:
-
-### Claude Code (full support — MCP + skills + hooks)
-
-```bash
-claude mcp add gitnexus -- npx -y gitnexus@latest mcp
-```
-
-### Cursor / Windsurf
-
-Add to `~/.cursor/mcp.json` (global — works for all projects):
-
-```json
-{
-  "mcpServers": {
-    "gitnexus": {
-      "command": "npx",
-      "args": ["-y", "gitnexus@latest", "mcp"]
-    }
-  }
-}
-```
-
-### OpenCode
-
-Add to `~/.config/opencode/config.json`:
-
-```json
-{
-  "mcp": {
-    "gitnexus": {
-      "command": "npx",
-      "args": ["-y", "gitnexus@latest", "mcp"]
-    }
-  }
-}
-```
-
-## How It Works
-
-GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:
-
-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 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
-
-The result is a **KuzuDB graph database** stored locally in `.gitnexus/` with full-text search and semantic embeddings.
-
-## MCP Tools
-
-Your AI agent gets these tools automatically:
-
-| Tool | What It Does | `repo` Param |
-|------|-------------|--------------|
-| `list_repos` | Discover all indexed repositories | — |
-| `query` | Process-grouped hybrid search (BM25 + semantic + RRF) | Optional |
-| `context` | 360-degree symbol view — categorized refs, process participation | Optional |
-| `impact` | Blast radius analysis with depth grouping and confidence | Optional |
-| `detect_changes` | Git-diff impact — maps changed lines to affected processes | Optional |
-| `rename` | Multi-file coordinated rename with graph + text search | Optional |
-| `cypher` | Raw Cypher graph queries | Optional |
-
-> With one indexed repo, the `repo` param is optional. With multiple, specify which: `query({query: "auth", repo: "my-app"})`.
-
-## MCP Resources
-
-| Resource | Purpose |
-|----------|---------|
-| `gitnexus://repos` | List all indexed repositories (read first) |
-| `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 |
-
-## MCP Prompts
-
-| 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 |
-
-## 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 --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
-gitnexus status                  # Show index status for current repo
-gitnexus clean                   # Delete index for current repo
-gitnexus clean --all --force     # Delete all indexes
-gitnexus wiki [path]             # Generate LLM-powered docs from knowledge graph
-gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
-```
-
-## 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, Swift
-
-## Agent Skills
-
-GitNexus ships with skill files that teach AI agents how to use the tools effectively:
-
-- **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
-
-Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global).
-
-## Requirements
-
-- Node.js >= 18
-- Git repository (uses git for commit tracking)
-
-## Privacy
-
-- All processing happens locally on your machine
-- No code is sent to any server
-- Index stored in `.gitnexus/` inside your repo (gitignored)
-- Global registry at `~/.gitnexus/` stores only paths and metadata
-
-## Web UI
-
-GitNexus also has a browser-based UI at [gitnexus.vercel.app](https://gitnexus.vercel.app) — 100% client-side, your code never leaves the browser.
-
-**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.
-
-## License
-
-[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/)
-
-Free for non-commercial use. Contact for commercial licensing.
+# GitNexus
+
+**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**, **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/)
+
+---
+
+## Why?
+
+AI coding tools don't understand your codebase structure. They edit a function without knowing 47 other functions depend on it. GitNexus fixes this by **precomputing every dependency, call chain, and relationship** into a queryable graph.
+
+**Three commands to give your AI agent full codebase awareness.**
+
+## Quick Start
+
+```bash
+# Index your repo (run from repo root)
+npx gitnexus analyze
+```
+
+That's it. This indexes the codebase, installs agent skills, registers Claude Code hooks, and creates `AGENTS.md` / `CLAUDE.md` context files — all in one command.
+
+To configure MCP for your editor, run `npx gitnexus setup` once — or set it up manually below.
+
+`gitnexus setup` auto-detects your editors and writes the correct global MCP config. You only need to run it once.
+
+### Editor Support
+
+| Editor | MCP | Skills | Hooks (auto-augment) | Support |
+|--------|-----|--------|---------------------|---------|
+| **Claude Code** | Yes | Yes | Yes (PreToolUse) | **Full** |
+| **Cursor** | Yes | Yes | — | MCP + Skills |
+| **Windsurf** | Yes | — | — | MCP |
+| **OpenCode** | Yes | Yes | — | MCP + Skills |
+
+> **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
+
+| Agent | Install | Source |
+|-------|---------|--------|
+| [pi](https://pi.dev) | `pi install npm:pi-gitnexus` | [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus) |
+
+## MCP Setup (manual)
+
+If you prefer to configure manually instead of using `gitnexus setup`:
+
+### Claude Code (full support — MCP + skills + hooks)
+
+```bash
+claude mcp add gitnexus -- npx -y gitnexus@latest mcp
+```
+
+### Cursor / Windsurf
+
+Add to `~/.cursor/mcp.json` (global — works for all projects):
+
+```json
+{
+  "mcpServers": {
+    "gitnexus": {
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
+    }
+  }
+}
+```
+
+### OpenCode
+
+Add to `~/.config/opencode/config.json`:
+
+```json
+{
+  "mcp": {
+    "gitnexus": {
+      "command": "npx",
+      "args": ["-y", "gitnexus@latest", "mcp"]
+    }
+  }
+}
+```
+
+## How It Works
+
+GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:
+
+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 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
+
+The result is a **KuzuDB graph database** stored locally in `.gitnexus/` with full-text search and semantic embeddings.
+
+## MCP Tools
+
+Your AI agent gets these tools automatically:
+
+| Tool | What It Does | `repo` Param |
+|------|-------------|--------------|
+| `list_repos` | Discover all indexed repositories | — |
+| `query` | Process-grouped hybrid search (BM25 + semantic + RRF) | Optional |
+| `context` | 360-degree symbol view — categorized refs, process participation | Optional |
+| `impact` | Blast radius analysis with depth grouping and confidence | Optional |
+| `detect_changes` | Git-diff impact — maps changed lines to affected processes | Optional |
+| `rename` | Multi-file coordinated rename with graph + text search | Optional |
+| `cypher` | Raw Cypher graph queries | Optional |
+
+> With one indexed repo, the `repo` param is optional. With multiple, specify which: `query({query: "auth", repo: "my-app"})`.
+
+## MCP Resources
+
+| Resource | Purpose |
+|----------|---------|
+| `gitnexus://repos` | List all indexed repositories (read first) |
+| `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 |
+
+## MCP Prompts
+
+| 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 |
+
+## 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 --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
+gitnexus status                  # Show index status for current repo
+gitnexus clean                   # Delete index for current repo
+gitnexus clean --all --force     # Delete all indexes
+gitnexus wiki [path]             # Generate LLM-powered docs from knowledge graph
+gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
+```
+
+## 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, Swift
+
+## Agent Skills
+
+GitNexus ships with skill files that teach AI agents how to use the tools effectively:
+
+- **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
+
+Installed automatically by both `gitnexus analyze` (per-repo) and `gitnexus setup` (global).
+
+## Requirements
+
+- Node.js >= 18
+- Git repository (uses git for commit tracking)
+
+## Privacy
+
+- All processing happens locally on your machine
+- No code is sent to any server
+- Index stored in `.gitnexus/` inside your repo (gitignored)
+- Global registry at `~/.gitnexus/` stores only paths and metadata
+
+## Web UI
+
+GitNexus also has a browser-based UI at [gitnexus.vercel.app](https://gitnexus.vercel.app) — 100% client-side, your code never leaves the browser.
+
+**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.
+
+## License
+
+[PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/)
+
+Free for non-commercial use. Contact for commercial licensing.

package/dist/cli/ai-context.js

@@ -25,83 +25,101 @@ const GITNEXUS_END_MARKER = '<!-- gitnexus:end -->';
  * - Self-review checklist — forces model to verify its own work
  */
 function generateGitNexusContent(projectName, stats) {
-    return `${GITNEXUS_START_MARKER}
-# GitNexus — Code Intelligence
-
-This project is indexed by GitNexus as **${projectName}** (${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
-
-> If any GitNexus tool warns the index is stale, run \`npx gitnexus analyze\` in terminal first.
-
-## Always Do
-
-- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`gitnexus_impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
-- **MUST run \`gitnexus_detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows.
-- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
-- When exploring unfamiliar code, use \`gitnexus_query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
-- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`gitnexus_context({name: "symbolName"})\`.
-
-## When Debugging
-
-1. \`gitnexus_query({query: "<error or symptom>"})\` — find execution flows related to the issue
-2. \`gitnexus_context({name: "<suspect function>"})\` — see all callers, callees, and process participation
-3. \`READ gitnexus://repo/${projectName}/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/${projectName}/context\` | Codebase overview, check index freshness |
-| \`gitnexus://repo/${projectName}/clusters\` | All functional areas |
-| \`gitnexus://repo/${projectName}/processes\` | All execution flows |
-| \`gitnexus://repo/${projectName}/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
-
-## CLI
-
-- Re-index: \`npx gitnexus analyze\`
-- Check freshness: \`npx gitnexus status\`
-- Generate docs: \`npx gitnexus wiki\`
-
+    return `${GITNEXUS_START_MARKER}
+# GitNexus — Code Intelligence
+
+This project is indexed by GitNexus as **${projectName}** (${stats.nodes || 0} symbols, ${stats.edges || 0} relationships, ${stats.processes || 0} execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
+
+> If any GitNexus tool warns the index is stale, run \`npx gitnexus analyze\` in terminal first.
+
+## Always Do
+
+- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run \`gitnexus_impact({target: "symbolName", direction: "upstream"})\` and report the blast radius (direct callers, affected processes, risk level) to the user.
+- **MUST run \`gitnexus_detect_changes()\` before committing** to verify your changes only affect expected symbols and execution flows.
+- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
+- When exploring unfamiliar code, use \`gitnexus_query({query: "concept"})\` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
+- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use \`gitnexus_context({name: "symbolName"})\`.
+
+## When Debugging
+
+1. \`gitnexus_query({query: "<error or symptom>"})\` — find execution flows related to the issue
+2. \`gitnexus_context({name: "<suspect function>"})\` — see all callers, callees, and process participation
+3. \`READ gitnexus://repo/${projectName}/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/${projectName}/context\` | Codebase overview, check index freshness |
+| \`gitnexus://repo/${projectName}/clusters\` | All functional areas |
+| \`gitnexus://repo/${projectName}/processes\` | All execution flows |
+| \`gitnexus://repo/${projectName}/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
+
+- Re-index: \`npx gitnexus analyze\`
+- Check freshness: \`npx gitnexus status\`
+- Generate docs: \`npx gitnexus wiki\`
+
 ${GITNEXUS_END_MARKER}`;
 }
 /**
@@ -193,16 +211,16 @@ async function installSkills(repoPath) {
             }
             catch {
                 // Fallback: generate minimal skill content
-                skillContent = `---
-name: ${skill.name}
-description: ${skill.description}
----
-
-# ${skill.name.charAt(0).toUpperCase() + skill.name.slice(1)}
-
-${skill.description}
-
-Use GitNexus tools to accomplish this task.
+                skillContent = `---
+name: ${skill.name}
+description: ${skill.description}
+---
+
+# ${skill.name.charAt(0).toUpperCase() + skill.name.slice(1)}
+
+${skill.description}
+
+Use GitNexus tools to accomplish this task.
 `;
             }
             await fs.writeFile(skillPath, skillContent, 'utf-8');

package/dist/cli/analyze.js

@@ -242,6 +242,13 @@ export const analyzeCommand = async (inputPath, options) => {
     }
     // ── 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,
@@ -252,6 +259,7 @@ export const analyzeCommand = async (inputPath, options) => {
             edges: stats.edges,
             communities: pipelineResult.communityResult?.stats.totalCommunities,
             processes: pipelineResult.processResult?.stats.totalProcesses,
+            embeddings: embeddingCount,
         },
     };
     await saveMeta(storagePath, meta);