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code analysis platform — builds a Knowledge Graph from source code with Web UI, HTTP API, CLI, and MCP server","maintainers":[{"name":"vohongtho.infotech","email":"vohongtho.infotech@gmail.com"}],"readme":"# Code Intelligence Platform\n\n[![npm version](https://img.shields.io/badge/npm-v1.0.10-blue)](https://www.npmjs.com/package/@vohongtho.infotech/code-intel)\n\nA static code analysis platform that builds a **Knowledge Graph** from your source code and makes it explorable through a Web UI, HTTP API, CLI, and MCP server.\n\n![Code Intelligence Platform](screenshots/explorer-overview.png)\n\n---\n\n## ✨ Features\n\n- **Knowledge Graph** — parses 15 languages into nodes (functions, classes, files, etc.) and edges (calls, imports, extends, etc.)\n- **Force-directed Graph Explorer** — interactive Sigma.js visualization with color-coded node types, hover highlighting, and filters\n- **Graph Query Language (GQL)** — query your codebase with `FIND`, `TRAVERSE`, `PATH`, `COUNT GROUP BY`; CLI, HTTP API, and MCP tool\n- **Source Code Preview** — click any node to open syntax-highlighted source at the exact line; \"Open in editor\" (`vscode://`) button\n- **Query Console** — web UI panel with GQL editor, sortable results table, query history, example queries, aggregate-safe rendering, and panel-scoped error containment\n- **AI-Generated Symbol Summaries** — optional `--summarize` flag generates 1-2 sentence summaries per symbol via OpenAI, Anthropic, or Ollama; cached by code hash\n- **Hybrid Search (BM25 + Vector RRF)** — Reciprocal Rank Fusion of keyword + semantic search; `searchMode: 'bm25' | 'vector' | 'hybrid'` in response\n- **Semantic Vector Search** — embeddings via `all-MiniLM-L6-v2`; enriched with summaries when available\n- **Code AI Chat** — grounded assistant that cites source files in every answer\n- **File Watcher & Auto-Reindex** — `code-intel watch` detects file saves and patches the live graph within ~1 second; WebSocket push notifies connected clients\n- **Code Health** — `code-intel health` reports dead code, circular dependencies (Tarjan SCC), god nodes, orphan files, and a 0–100 health score\n- **HTTP API** — REST endpoints for graph, search, inspect, blast radius, flows, query, source, health\n- **MCP Server** — Model Context Protocol integration for LLM tooling with 6 new reasoning tools (`explain_relationship`, `pr_impact`, `similar_symbols`, `health_report`, `suggest_tests`, `cluster_summary`), pagination, and tool-chaining hints\n- **Security & Quality Scanning** — `code-intel secrets` (hardcoded API keys, DB URLs, RSA keys), `code-intel scan` (SQL Injection CWE-89, XSS CWE-79, SSRF CWE-918, Path Traversal CWE-22, Command Injection CWE-78), `--format sarif` for CI integration\n- **Complexity Metrics** — `code-intel complexity --top N` ranks functions by cyclomatic + cognitive complexity; `complexity_hotspots` MCP tool\n- **Test Coverage Gaps** — `code-intel coverage` lists untested exported symbols sorted by blast radius; `--threshold <pct>` fails CI if below target\n- **Deprecated API Detection** — `code-intel deprecated` finds usages of `@deprecated` JSDoc, `@Deprecated` (Java), `#[deprecated]` (Rust), and built-in Node.js deprecated APIs\n- **CLI** — analyze, serve, watch, query, search, inspect, impact, health commands with animated `█░` progress bars and braille spinners\n- **Multi-language** — TypeScript, JavaScript, Python, Java, Go, C, C++, C#, Rust, PHP, Ruby, Swift, Kotlin, Dart, HTML (15 languages via tree-sitter AST)\n- **Truthful capability states** — language capability reporting distinguishes `supported`, `partial`, `not-applicable`, and `unsupported` so grammar availability is not mistaken for semantic completeness\n- **Incremental Analysis** — `--incremental` flag re-parses only git-changed/mtime-changed files; 10k-file repo with 3 changes: 288ms\n- **Parallel Analysis** — `--parallel` flag runs parse + resolve phases on worker threads for large repos\n- **Selection-aware AI Context Files** — the first interactive `code-intel analyze` stores the selected agents in `.code-intel/agent-targets.json`; later analyses update only those selected repository instruction files, such as `AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md`, `.cursor/rules/code-intel.mdc`, `.kiro/steering/code-intel.md`, `.clinerules`, `.windsurfrules`, `.kilocode/rules/code-intel-rules.md`, or `.agents/rules/code-intel-rules.md`\n- **Agent-aware Setup** _(v1.0.10)_ — `code-intel setup [path]` reads `.code-intel/agent-targets.json`, configures MCP independently, and installs only supported global hooks/plugins for agents selected during analysis. Setup never creates repository-scoped `.cursor`, `.github`, `.kilocode`, `.agents`, `.clinerules`, `.windsurfrules`, `AGENTS.md`, or similar instruction files\n- **Repository Groups** — multi-repo / monorepo service tracking with workspace auto-discovery (npm, pnpm, Nx, Turborepo), contract extraction (OpenAPI, GraphQL, Protobuf), type-aware similarity scoring, and cross-repo dependency detection\n  - **OpenAPI note:** contract extraction currently parses **JSON** OpenAPI/Swagger specs. YAML filenames are discovered, but YAML parsing is not implemented in `v1.0.4`.\n- **`.codeintelignore`** — exclude directories from analysis (like `.gitignore` but for code-intel)\n- **Structured Logging** — winston-based logger with daily-rotating log files at `~/.code-intel/logs/`, sensitive-data masking, and configurable log levels\n- **Performance** — parallel batch file I/O, shared file cache (zero double-reads), O(log n) binary-search enclosing-function lookup\n- **`code-intel init` Wizard** _(v0.9)_ — interactive 5-step setup wizard; creates `~/.code-intel/config.json` with editor MCP registration, LLM provider, embeddings, auth mode, and port settings\n- **Config Management CLI** _(v0.9)_ — `config get/set/list/validate/reset` with JSON Schema, `$ENV_VAR` expansion, and masked secret output\n- **Better Error Messages** _(v0.9)_ — `CI-XXXX` error codes, actionable hints, `--debug` stack traces, startup prerequisite checks\n- **Shell Completion** _(v0.9)_ — `code-intel completion bash|zsh|fish`; dynamic repo + group name completion; `setup --completion` auto-installs\n- **VS Code Extension** _(v0.9)_ — symbol hover tooltips, Symbol Explorer panel, status bar freshness indicator, \"Open in Graph\" command, command palette integration\n- **Self-Update** _(v0.9)_ — `code-intel update` checks npm registry; background version check on startup; `--no-update-check` to suppress\n- **`--dry-run` flag** _(v0.9)_ — `analyze`, `clean`, `group sync` preview what would happen without side effects\n- **`code-intel doctor`** _(v0.9)_ — full diagnostics: Node.js, git, config, registry, DB integrity, network; exit 1 on any failure\n- **Lazy Graph Loading** _(v1.0)_ — `serve` starts in <2s for 10k-file repos; LRU node cache (5,000 nodes by default, `GRAPH_CACHE_SIZE` env var); background warm of high-blast-radius nodes\n- **Pre-Built BM25 Index** _(v1.0)_ — inverted index built at analysis time; loaded into memory on `serve` startup; 2,000+ q/s throughput; incremental-only updates on re-index\n- **Memory-Efficient Graph** _(v1.0)_ — `Int32Array`-packed adjacency + symbol interning = ≥30% memory reduction; `--max-memory <MB>` flag spills node content to DB\n- **Pipeline Profiling** _(v1.0)_ — `analyze --profile` writes `.code-intel/profile.json`; per-phase heap memory captured; bottleneck warning if any phase >50% of total; verbose timing table\n- **Load & Soak Tests** _(v1.0)_ — nightly CI load tests (1k/10k fixture repos), weekly soak tests (memory stability, watcher throughput), regression gate: >20% regression fails CI; `tests/perf/baseline.json` committed to repo\n- **Graceful Degradation** _(v1.0)_ — `X-Stale`/`X-Stale-Since` headers on DB outage; LLM-unavailable summarize skip; MCP tool timeout → `{ truncated: true }`; watcher crash recovery; worker crash retry\n  - **Worker note for v1.0.4:** parallel analysis retries worker crashes, but `v1.0.4` does not introduce a new user-facing worker timeout control. Treat long/stalled analysis as runtime investigation, not documented timeout recovery behavior.\n- **Token-Efficient MCP** _(v1.0.1)_ — compact JSON responses (null/undefined stripped); MCP tool defaults tuned for LLM sessions: `search`/`file_symbols`/`list_exports` default 10 results (was 50), `blast_radius`/`pr_impact` default 2 hops (was 5); `suggested_next_tools` opt-in via `CODE_INTEL_SUGGEST_NEXT_TOOLS=true`; ~63% fewer tokens per typical 5-tool session\n- **Context Builder** _(v1.0.1)_ — `src/context/builder.ts` builds structured `[SUMMARY]` / `[LOGIC]` / `[RELATION]` / `[FOCUS CODE]` documents from seed symbols in ≤50% of v1.0.0 token cost; query-intent presets (`code`, `callers`, `architecture`, `auto`); adaptive snippets; cross-block dedup; `code-intel context <symbols...> --show-context`\n- **Enforced Tool Policy in AI Context Files** _(v1.0.1)_ — `AGENTS.md`/`CLAUDE.md`/`copilot-instructions.md`/`.cursor/rules`/`.kiro/steering` now include a `TOOL POLICY: ENFORCED` block forbidding raw `grep`/`find`/`cat` in favour of `code-intel search` → `inspect` → `impact`; saves ~3,000 tokens per cold-file lookup\n\n---\n\n## 🚀 Quick Start\n\n### Requirements\n\n- **Node.js** 22.17+\n- **npm** 10+\n\n---\n\n### Option A — Install globally from npm _(recommended)_\n\n```bash\nnpm install -g @vohongtho.infotech/code-intel\n```\n\n> **Default secret storage:** the CLI stores secrets in the encrypted `.code-intel/.secrets` file backend. No OS keychain package is required for the default install.\n>\n> **Upgrade note for v1.0.4:** After upgrading, re-build the local index before comparing results or using `serve`/`status` against old data:\n>\n> ```bash\n> code-intel analyze --force\n> ```\n>\n> This refreshes `.code-intel/graph.db` and `.code-intel/meta.json`. Comparing fresh CLI behavior against stale indexes can look like a regression when it is only old index state.\n\nVerify the installation:\n\n```bash\ncode-intel --version\n```\n\n---\n\n### Option B — Build from source\n\nUse this if you want to develop, modify, or contribute to the platform.\n\n**1. Clone the repository**\n\n```bash\ngit clone https://github.com/vohongtho/code-intel-platform.git\ncd code-intel-platform\n```\n\n**2. Install all workspace dependencies**\n\n```bash\nnpm install\n```\n\n**3. Build all packages** (shared → core → web)\n\n```bash\nnpm run build\n```\n\nThis runs `tsup` for the core package (outputs to `code-intel/core/dist/`) and `vite` for the web UI (outputs to `code-intel/web/dist/`).\n\n**4. Install the built CLI globally**\n\n```bash\nnpm install -g ./code-intel/core\n```\n\nVerify:\n\n```bash\ncode-intel --version\n```\n\n> **Tip:** After making code changes, re-run `npm run build` — the CLI picks up the new build automatically since the global install points to the local `dist/` folder.\n\n---\n\n### Option C — Build locally & install globally _(CI / automation)_\n\nUse this approach in CI pipelines, Docker images, or any environment where you need a clean, self-contained global install from local source without a persistent `node_modules` link.\n\n**1. Clone & install dependencies**\n\n```bash\ngit clone https://github.com/vohongtho/code-intel-platform.git\ncd code-intel-platform\nnpm install\n```\n\n**2. Build all packages**\n\n```bash\nnpm run build\n```\n\n**3. Pack the core package into a tarball**\n\n```bash\ncd code-intel/core\nnpm pack\n# produces: vohongtho.infotech-code-intel-0.1.4.tgz (version number may vary)\ncd ../..\n```\n\n**4. Install the tarball globally**\n\n```bash\nnpm install -g code-intel/core/vohongtho.infotech-code-intel-*.tgz\n```\n\n**5. Verify**\n\n```bash\ncode-intel --version\n```\n\n#### One-liner (copy-paste for CI scripts)\n\n```bash\ngit clone https://github.com/vohongtho/code-intel-platform.git && \\\n  cd code-intel-platform && \\\n  npm install && \\\n  npm run build && \\\n  npm pack --workspace=code-intel/core && \\\n  npm install -g vohongtho.infotech-code-intel-*.tgz\n```\n\n#### Docker example\n\n```dockerfile\nFROM node:22-bookworm-slim\n\nRUN git clone https://github.com/vohongtho/code-intel-platform.git /opt/code-intel && \\\n    cd /opt/code-intel && \\\n    npm install && \\\n    npm run build && \\\n    npm pack --workspace=code-intel/core && \\\n    npm install -g vohongtho.infotech-code-intel-*.tgz && \\\n    rm -rf /opt/code-intel\n\nWORKDIR /workspace\nENTRYPOINT [\"code-intel\"]\n```\n\n> **Why pack instead of `npm install -g ./code-intel/core`?**\n> `npm pack` produces a standalone tarball containing only the published `files` (the `dist/` folder + `package.json`). This mirrors exactly what is published to npm and avoids bringing in dev symlinks or workspace hoisting artefacts.\n\n---\n\n### Analyze & Serve\n\n```bash\n# First, analyze the project to build the index\ncode-intel analyze\n\n# Then start the server (requires an existing index)\ncode-intel serve\n\n# Or with a specific path and port\ncode-intel analyze ./my-project\ncode-intel serve ./my-project --port 4747\n```\n\nThen open **http://localhost:4747** in your browser — the Web UI auto-connects and loads the graph.\n\n### After analysis\n\n`code-intel analyze` automatically generates or updates:\n- **`AGENTS.md`** + **`CLAUDE.md`** — AI context files with a concise `code-intel` guidance block. These files are managed with **surgical precision**:\n  - **File does not exist** → created from a template with a managed block and a clearly marked section for your own notes\n  - **File exists with markers** → only the `<!-- code-intel:start -->…<!-- code-intel:end -->` block is updated; all your custom content is preserved untouched\n  - **File exists without markers** → the block is appended at the end; existing content is never overwritten\n\n### Exclude directories\n\nCreate a `.codeintelignore` file in your project root:\n\n```\n# one directory name per line\nvendor\ngenerated\nfixtures\n```\n\n---\n\n## 🤖 MCP and agent setup\n\nRepository instruction files are selected and generated by `code-intel analyze`. On the first interactive analysis, the selected agents are stored in:\n\n```text\n.code-intel/agent-targets.json\n```\n\nRun setup for that repository:\n\n```bash\ncode-intel setup [path]\n```\n\nSetup performs two independent operations:\n\n1. **MCP configuration** — configures/displays the Code Intel MCP server entry.\n2. **Selected global integrations** — installs only the supported global hook or plugin integrations mapped to agents saved by analysis.\n\nSetup does **not** create or modify repository instruction files such as `.cursor/**`, `.github/**`, `.kilocode/**`, `.agents/**`, `.clinerules`, `.windsurfrules`, `AGENTS.md`, or `CLAUDE.md`. Existing files are left unchanged.\n\nUseful modes:\n\n```bash\ncode-intel setup ./services/api     # Use that repository's saved selection\ncode-intel setup --mcp-only         # Configure MCP only\ncode-intel setup --all-agents       # Install all supported global integrations\ncode-intel setup --dry-run          # Show the plan without writing files\n```\n\nWhen the selection file is missing or invalid, agent integration installation fails closed and never falls back to every agent. Run `code-intel analyze` to create the repository selection, then rerun setup.\n\n> The `code-intel-hook` binary can rewrite supported shell lookups such as `grep MyClass src/` into structured Code Intel searches. Installers remain idempotent and preserve existing user configuration.\n\n---\n\n## 🖥️ Web UI\n\n| Panel | Description |\n|-------|-------------|\n| **Explorer** | Graph composition stats, search results, overview counters |\n| **Filters** | Toggle node/edge types, set focus depth |\n| **Files** | Recursive file tree with search filter and file icons |\n| **Group** | Multi-repo group view with contracts and cross-repo links (visible when in group mode) |\n| **Graph Canvas** | Force-directed graph, click nodes to inspect, hover to highlight neighbors |\n| **Code AI** | Chat with grounded answers citing source file locations |\n\n### Search Modes\n\n- **Keyword** (default) — BM25-like text search across node names and content\n- **⚡ vec** — Semantic vector search using embeddings (auto-built in background after server starts)\n\nToggle between modes using the `vec` button in the header search bar.\n\n---\n\n## 📦 Architecture\n\n```\ncode-intel-platform/\n├── code-intel/\n│   ├── shared/                    # Shared types published alongside core\n│   │   └── src/\n│   │       ├── graph-types.ts     # CodeNode, CodeEdge, NodeKind, EdgeKind\n│   │       ├── languages.ts       # Language enum (14 languages)\n│   │       ├── pipeline-types.ts  # PipelineContext, PhaseResult\n│   │       └── detection.ts       # Language detection helpers\n│   │\n│   ├── core/                      # Backend: pipeline, parsers, HTTP API, MCP, CLI, storage\n│   │   └── src/\n│   │       ├── pipeline/          # 6-phase DAG orchestrator + DAG validator\n│   │       │   └── phases/        # scan · structure · parse · resolve · cluster · flow\n│   │       │\n│   │       ├── parsing/           # Tree-sitter AST parsing layer\n│   │       │   ├── parser-manager.ts   # Loads + caches tree-sitter parsers\n│   │       │   ├── ast-cache.ts        # AST memoization\n│   │       │   ├── query-runner.ts     # Executes tree-sitter queries\n│   │       │   └── queries/            # Per-language query files (14 languages)\n│   │       │\n│   │       ├── languages/         # Language registry + per-language extraction modules\n│   │       │   ├── registry.ts         # Maps file extension → language module\n│   │       │   └── modules/            # ts · js · py · java · go · rs · c · cpp · cs\n│   │       │                           # php · kt · rb · swift · dart\n│   │       │\n│   │       ├── resolver/          # Import resolution (edges between files/symbols)\n│   │       │   ├── import-resolver.ts\n│   │       │   ├── binding-tracker.ts\n│   │       │   └── strategies/    # relative-path · package-lookup · namespace-alias · wildcard-expand\n│   │       │\n│   │       ├── call-graph/        # Call edge builder + call classifier\n│   │       ├── inheritance/       # Heritage builder, MRO walker, override detector\n│   │       ├── scope-analysis/    # Scope builder (variable / binding scope trees)\n│   │       ├── clustering/        # Directory-based community detection\n│   │       ├── flow-detection/    # Entry-point finder + execution flow tracer\n│   │       │\n│   │       ├── graph/             # In-memory knowledge graph (O(1) node/edge lookup)\n│   │       ├── search/            # BM25 text search · vector embedder · vector index (LadybugDB)\n│   │       ├── storage/           # LadybugDB graph persistence · repo registry · metadata\n│   │       │\n│   │       ├── multi-repo/        # Repository groups, contract extraction, cross-repo linking\n│   │       │   ├── group-registry.ts   # Load/save group configs + sync results\n│   │       │   ├── group-sync.ts       # Extract contracts + match via RRF\n│   │       │   ├── group-query.ts      # Cross-repo BM25 search with RRF merge\n│   │       │   └── types.ts            # RepoGroup, Contract, ContractLink, GroupSyncResult\n│   │       │\n│   │       ├── http/              # Express REST API + static web UI serving\n│   │       ├── mcp-server/        # MCP stdio transport + all tool/resource handlers\n│   │       ├── shared/            # Logger (winston, sensitive-data masking, ~/.code-intel/logs/)\n│   │       └── cli/               # Commander CLI (progress bars, spinners)\n│   │           ├── main.ts              # All CLI commands\n│   │           └── context-writer.ts    # Upserts AGENTS.md + CLAUDE.md blocks\n│   │\n│   └── web/                       # React + Sigma.js frontend\n│       └── src/\n│           ├── pages/             # ConnectPage · LoadingPage · ExplorerPage\n│           ├── components/\n│           │   ├── graph/         # GraphView (Sigma.js force-directed canvas)\n│           │   ├── panels/        # NodeDetail · SearchBar · SidebarChat · SidebarFiles · SidebarFilters\n│           │   └── shared/        # Header · StatusFooter · KeyboardShortcutsModal\n│           ├── ai/                # Chat agent with intent parsing + tool calls\n│           ├── api/               # ApiClient (search, vector-search, inspect, blast-radius, flows, clusters)\n│           ├── graph/             # Node color palette + ForceAtlas2 layout utilities\n│           └── state/             # React context + reducer (AppContext, AppState)\n│\n├── .code-intel/                   # Generated per-repo: graph.db · vector.db · meta.json\n└── .codeintelignore               # Optional: directories to exclude (like .gitignore)\n```\n\n### Pipeline Phases\n\n| Phase | Description |\n|-------|-------------|\n| `scan` | Walk filesystem, collect source files (parallel batch I/O, 512 KB limit), ignore `node_modules`, `dist`, `.venv`, etc. |\n| `structure` | Create file and directory nodes in the graph |\n| `parse` | Read files in parallel batches of 64, extract symbols (functions, classes, etc.), build per-file sorted function index |\n| `resolve` | Resolve imports → edges, build call graph (O(log n) binary-search lookup), detect heritage (extends/implements) |\n| `cluster` | Directory-based community detection, add cluster nodes |\n| `flow` | Detect entry points, trace execution flows |\n| `summarize` | _(opt-in)_ Generate 1–2 sentence AI summaries for `function`/`class`/`method`/`interface` nodes via OpenAI, Anthropic, or Ollama; skips unchanged nodes (code-hash cache) |\n\nEach phase streams live progress to the CLI via animated `█░` progress bars:\n\n```\n  [parse    ] ████████████████░░░░░░░░░░░░░░  53% (80/151)\n```\n\nPost-pipeline steps (DB persist, context files) show a braille spinner:\n\n```\n  ⠹ Persisting graph to DB…\n```\n\n---\n\n## 📋 Logging\n\nLogs are written to **`~/.code-intel/logs/`** using daily rotation (powered by [winston](https://github.com/winstonjs/winston)):\n\n| Setting | Default | Override |\n|---------|---------|----------|\n| Log directory | `~/.code-intel/logs/` | — |\n| Log file pattern | `YYYY-MM-DD-code-intel.log` | — |\n| Max file size | 20 MB | — |\n| Retention | 14 days | — |\n| Log level | `info` | `LOG_LEVEL=debug\\|info\\|warn\\|error\\|silent` |\n| Production mode | Console only | `NODE_ENV=production` |\n\nSensitive data (passwords, tokens, API keys, emails, credit cards, etc.) is automatically **masked** before writing — only the first and last character are visible.\n\n---\n\n## 🛠️ CLI Commands\n\n### Setup\n\n```bash\ncode-intel setup [path]                  # Configure MCP and selected-agent global integrations\ncode-intel setup --mcp-only              # Configure MCP without agent integrations\ncode-intel setup --all-agents            # Install every supported global integration\ncode-intel setup --dry-run               # Print the plan without writing files\n```\n\nProject instruction files are generated only by `code-intel analyze` from the saved repository agent selection.\n\n### Analyze\n\n```bash\ncode-intel analyze [path]                # Parse source code and auto-use incremental mode when prior metadata makes it safe\ncode-intel analyze --force               # Discard existing index and perform a full re-analysis\ncode-intel analyze --embeddings          # Build a vector index and remember embeddings for this repo\ncode-intel analyze --skip-embeddings     # Skip embedding generation for this run only\ncode-intel analyze --skip-agents-md      # Preserve any hand-edited content in AGENTS.md / CLAUDE.md\n```\n\nSticky embeddings behavior:\n\n- The first successful `code-intel analyze --embeddings` run stores the repo preference in `.code-intel/meta.json`.\n- Later `code-intel analyze`, `code-intel analyze --incremental`, and `code-intel analyze --force` runs auto-enable embeddings for that repo unless you pass `--skip-embeddings`.\n- Plain `code-intel analyze` now auto-attempts incremental graph reindexing when valid prior `.code-intel/meta.json` exists and incremental safety checks pass; otherwise it falls back to full analysis.\n- Successful incremental runs preserve full-repository stats in `.code-intel/meta.json`; a second no-change analyze refreshes metadata without zeroing `graph.db` or `bm25.db`.\n- A second `code-intel analyze --embeddings` run with no source changes now preserves the existing `vector.db` instead of rebuilding it; only changed or deleted files trigger incremental vector updates when the stored embedding fingerprint is still compatible.\n- Deleted files are removed from the next successful index snapshot, and `code-intel status` always reports full-repository node, edge, and file counts rather than changed-file subsets.\n- If `vector.db` is missing, stale, corrupted, or incompatible with the current embedding fingerprint, `code-intel analyze` rebuilds the full vector index automatically.\n- `--skip-embeddings` does not forget the repo preference; it skips vectors for that run and marks remembered embeddings stale until the next normal analyze.\n- Previously indexed repos with only a legacy `vector.db` upgrade in place on the next analyze; no manual migration command is required.\n\n```bash\ncode-intel analyze --skip-git            # Allow analysis of directories that are not Git repositories\ncode-intel analyze --verbose             # Print every file skipped due to an unsupported parser\n```\n\n### Server\n\n```bash\ncode-intel mcp [path]                    # Launch the MCP stdio server consumed by AI-enabled editors\ncode-intel serve [path] --port <n>       # Start the HTTP API and serve the interactive web UI (default :4747)\ncode-intel watch [path] --port <n>       # Start HTTP server + file watcher (auto-reindex on file saves)\n```\n\n### Query (GQL)\n\n```bash\ncode-intel query \"<gql>\"                 # Run a GQL query (FIND / TRAVERSE / PATH / COUNT GROUP BY)\ncode-intel query \"<gql>\" --format table|json|csv   # Output format (default: table)\ncode-intel query --file <path.gql>       # Load query from file\ncode-intel query \"<gql>\" --limit <n>     # Override LIMIT in the query\ncode-intel query --save <name> \"<gql>\"   # Save a named query to .code-intel/queries/\ncode-intel query --run <name>            # Run a saved query by name\ncode-intel query --list                  # List all saved queries\ncode-intel query --delete <name>         # Delete a saved query\n```\n\n### Health\n\n```bash\ncode-intel health [path]                 # Show health score + dead code / cycles / god nodes / orphans\ncode-intel health --dead-code            # List all dead-code symbols\ncode-intel health --cycles               # List all circular dependency cycles\ncode-intel health --orphans              # List all orphan files\ncode-intel health --json                 # Machine-readable JSON output\n```\n\n### Registry\n\n```bash\ncode-intel list                          # Display all repositories that have been indexed\ncode-intel status [path]                 # Report index freshness, symbol counts, and last-run duration\ncode-intel clean [path]                  # Remove the .code-intel/ index for the specified repository\ncode-intel clean --all --force           # Permanently remove all indexed repositories (requires --force)\n```\n\n### Exploration\n\n```bash\ncode-intel search <query>                # Execute a BM25 keyword search across all indexed symbols\ncode-intel search <query> --limit <n>    # Limit number of results (default: 20)\ncode-intel inspect <symbol>              # Show callers, callees, import edges, and source location\ncode-intel impact <symbol>               # Compute the transitive blast radius of a change to a symbol\ncode-intel impact <symbol> --depth <n>   # Set maximum traversal depth / hops (default: 5)\n```\n\n### Groups (multi-repo / monorepo service tracking)\n\n```bash\ncode-intel group create <name>                                              # Create a named group to track multiple repositories together\ncode-intel group add <group> <groupPath> <registryName>                    # Enroll an indexed repo in a group under the given hierarchy path\ncode-intel group remove <group> <groupPath>                                # Remove a repository from a group by its hierarchy path\ncode-intel group list [name]                                               # List all groups, or print the full membership of one group\ncode-intel group sync <name>                                               # Extract cross-repo contracts and resolve provider/consumer links\ncode-intel group contracts <name> [--kind] [--repo] [--min-confidence]    # Inspect extracted contracts and confidence-ranked cross-links\ncode-intel group query <name> <q>                                          # Run a merged RRF search across every repository in a group\ncode-intel group status <name>                                             # Audit index freshness and sync staleness for all group members\n```\n\n**`group add` parameters:**\n- `<group>` — name of the group\n- `<groupPath>` — hierarchy path (e.g. `hr/hiring/backend`)\n- `<registryName>` — the repo's name as shown by `code-intel list`\n\n**`group contracts` options:**\n- `--kind <kind>` — filter by contract kind: `export` | `route` | `schema` | `event`\n- `--repo <repo>` — filter by registry name\n- `--min-confidence <pct>` — minimum link confidence 0–100 (default: 0)\n\n---\n\n## 🌐 HTTP API\n\n| Method | Endpoint | Description |\n|--------|----------|-------------|\n| `GET`  | `/api/v1/health` | Server status, graph size, watcher state |\n| `GET`  | `/api/v1/repos` | List indexed repos |\n| `GET`  | `/api/v1/graph/:repoId` | Full graph (nodes + edges) |\n| `POST` | `/api/v1/search` | Canonical scoped search (`query`, `limit`, `mode`, `scope`) with repo/group targeting; repo scope uses `repoId` |\n| `POST` | `/api/v1/vector-search` | Deprecated compatibility alias for vector mode; returns resolved scope/mode metadata |\n| `GET`  | `/api/v1/vector-status` | Vector index ready/building status |\n| `GET`  | `/api/v1/nodes/:id` | Node detail (callers, callees, imports, etc.) |\n| `POST` | `/api/v1/blast-radius` | Impact analysis; request body accepts canonical `repoId` |\n| `POST` | `/api/v1/query` | Execute a GQL query string; accepts optional canonical `scope`, returns normalized `{ kind, nodes, edges, groups, path, executionTimeMs, truncated, totalCount, scope }` |\n| `POST` | `/api/v1/query/explain` | Return query plan without executing; accepts optional canonical `scope` |\n| `GET`  | `/api/v1/source` | Fetch file content with ±20 lines context; path-traversal protected; accepts optional `repoId` |\n| `POST` | `/api/v1/grep` | Regex search in file content |\n| `GET`  | `/api/v1/flows` | List detected flows; accepts optional `repoId` |\n| `GET`  | `/api/v1/clusters` | List clusters; accepts optional `repoId` |\n\nMigration note: internal/UI-owned repo selectors now use `repoId`. Legacy flat `repo` inputs remain only as bounded compatibility adapters on selected surfaces during migration.\n\n---\n\n## 🤖 MCP Server Tools\n\nAll tools are available to any MCP-capable editor (Claude Desktop, Claude Code, VS Code, Cursor, etc.) after running `code-intel setup`.\n\n### Core Tools\n\n| Tool | Input | Description |\n|------|-------|-------------|\n| `repos` | _(none)_ | List all indexed repositories with path, indexedAt, and node/edge counts |\n| `overview` | _(none)_ | Repository summary: total nodes/edges + full breakdown by kind. **Use this first** to understand the codebase shape. |\n| `search` | `query` (string), `limit` (number, default 10), `mode` (`auto`\\|`bm25`\\|`vector`, default `auto`), `scope` (object, optional), legacy `repo`/`group` during migration | Scoped search with MCP default behavior matching HTTP: hybrid/semantic when vector is ready, BM25 otherwise; explicit `mode` can force BM25 or prefer vector with BM25 fallback |\n| `inspect` | `symbol_name` (string) | 360° view of a symbol: definition, callers, callees, imports, heritage (extends/implements), members, cluster, and source preview |\n| `context` | `symbols` (string[]), `intent` (`code`\\|`callers`\\|`architecture`\\|`auto`, default `auto`), `max_tokens` (number, default/server max 6000), `limit` (number, default 10) | Token-budgeted deep context for one or more symbols: returns `summary`, `logic`, `relation`, `focusCode`, and `truncated` from the shared context builder |\n| `blast_radius` | `target` (string), `direction` (`callers`\\|`callees`\\|`both`), `max_hops` (number, default 5) | Impact analysis: traverse the call/import graph to find all affected symbols. Returns a `riskLevel` (LOW / MEDIUM / HIGH). |\n| `file_symbols` | `file_path` (string, partial match) | List all symbols defined in a file, ordered by line number. Avoids having to read raw source. |\n| `find_path` | `from` (string), `to` (string), `max_hops` (number, default 8) | Find the shortest call/import path between two symbols via BFS. |\n| `list_exports` | `kind` (string, optional), `limit` (number, default 100) | List all exported symbols — the public API surface of the codebase. Filter by kind: `function`, `class`, `interface`, etc. |\n| `routes` | _(none)_ | List all HTTP route handler mappings detected in the codebase |\n| `clusters` | `limit` (number, default 50) | List detected code clusters (directory-based communities) with member counts and top 10 symbols each |\n| `flows` | `limit` (number, default 50) | List detected execution flows with entry points, steps, and step counts |\n| `query` | `gql` (string), `limit` (number, optional) | Execute a GQL query (`FIND`, `TRAVERSE`, `PATH`, `COUNT GROUP BY`) against the live graph; returns normalized `{ kind, nodes, edges, groups, path, executionTimeMs, truncated, totalCount }` |\n| `detect_changes` | `base_ref` (string, default `HEAD`), `diff_text` (string, optional) | **Git-diff impact analysis**: maps changed lines to graph symbols and computes combined blast radius. Ideal for PR review or pre-commit checks. |\n| `raw_query` | `cypher` (string) | _(deprecated — use `query` instead)_ Simplified Cypher-like graph query: `name='X'` or `:kind` |\n\n### Group / Multi-Repo Tools\n\n| Tool | Input | Description |\n|------|-------|-------------|\n| `group_list` | `name` (string, optional) | List all configured repository groups, or show full membership of one group |\n| `group_sync` | `name` (string) | Extract contracts (exports, routes, schemas, events) from all member repos and detect cross-repo provider→consumer links via name matching + RRF scoring |\n| `group_contracts` | `name` (string), `kind` (`export`\\|`route`\\|`schema`\\|`event`, optional), `repo` (string, optional), `min_confidence` (number 0–1, optional) | Inspect extracted contracts and confidence-ranked cross-repo links from the last sync |\n| `group_query` | `name` (string), `query` (string), `limit` (number, default 10) | BM25 search across all repos in a group, merged via Reciprocal Rank Fusion. Returns unified ranked list + per-repo breakdown. |\n| `group_status` | `name` (string) | Check index freshness and sync staleness for all repos in a group. Flags repos as `OK`, `STALE` (>24h), or `NOT_INDEXED`. |\n\n### Resources\n\nMCP resources are readable via `ReadResource` — your editor can pull them as structured context.\n\n| URI | Description |\n|-----|-------------|\n| `codeintel://repo/<name>/overview` | Repository stats: total nodes, edges, and per-kind node counts |\n| `codeintel://repo/<name>/clusters` | All cluster nodes with member counts |\n| `codeintel://repo/<name>/flows` | All detected execution flows with entry points and steps |\n\n---\n\n## 💾 Storage\n\nAll generated files are stored locally — nothing is sent to external servers.\n\n| Path | Contents |\n|------|----------|\n| `.code-intel/graph.db` | LadybugDB knowledge graph |\n| `.code-intel/vector.db` | LadybugDB vector index |\n| `.code-intel/meta.json` | Index metadata (timestamp, stats) |\n| `~/.code-intel/registry.json` | Global registry of all indexed repos |\n| `~/.code-intel/groups/<name>.json` | Repository group configuration |\n| `~/.code-intel/groups/<name>.sync.json` | Last group sync results (contracts + cross-repo links) |\n| `~/.code-intel/logs/YYYY-MM-DD-code-intel.log` | Daily-rotating application logs (14-day retention) |\n\n---\n\n## 🧪 Testing\n\n```bash\nnpm run test\n```\n\n46 tests across unit + integration suites covering:\n- Knowledge graph operations\n- Language detection\n- Call classifier\n- MRO computation\n- Scope analysis\n- Text search\n- Pipeline integration (parse → resolve)\n\n---\n\n## 📊 Benchmark / Eval\n\nMeasure accuracy of the knowledge graph, MCP tools, and context file generation:\n\n```bash\n# Single-language fixture (TypeScript)\nnpm run eval\n\n# Multi-language fixture (Python + TypeScript)\nnpm run eval:multi\n\n# Run all fixtures\nnpm run eval:all\n\n# Save results as JSON\nnpm run eval:json\n```\n\nResults are written to `eval/results/`. Each run scores:\n\n| Phase | What is tested |\n|-------|---------------|\n| Analysis | Symbol count, edge count, exit code |\n| Search | BM25 keyword search accuracy |\n| Inspect | Symbol detail retrieval |\n| Impact | Blast radius correctness |\n| Context Files | AGENTS.md / CLAUDE.md upsert + idempotency |\n| Status | Index freshness reporting |\n| Clean | Index removal |\n\nCurrent score: **25/25 (100%)** TypeScript · **15/15 (100%)** multi-lang\n\n### Agent Benchmark (Before vs After)\n\nThe `bench` command simulates an AI agent answering code questions with and without code-intel:\n\n```bash\nnpm run bench\n```\n\nLatest results on the TypeScript fixture (6 tasks):\n\n| Metric | Baseline (grep + read files) | Enhanced (code-intel tools) | Δ |\n|--------|-----------------------------|-----------------------------|---|\n| **Accuracy** | 58% | **100%** | +42pp |\n| **Tool calls/task** | 2.0 | **1.0** | −50% |\n| **Response size** | 1023 chars | **189 chars** | −82% token cost |\n\n### MCP Server Benchmark\n\nTest all MCP tools directly over the JSON-RPC stdio transport:\n\n```bash\nnpm run bench:mcp\n```\n\nLatest results (19 cases, TypeScript fixture):\n\n| Metric | Result |\n|--------|--------|\n| **Score** | 19/19 (100%) |\n| **Avg tool latency** | 9ms/call |\n\nTools tested: `repos`, `search` (default / `bm25` / `vector`), `context`, `inspect`, `blast_radius`, `routes`, `raw_query` + `ListTools`, `ListResources`, `ReadResource`\n\n---\n\n## 🔧 Technical Implementation Details\n\n### web-tree-sitter v0.26 API\n\n- `Parser.SyntaxNode` → `Node` (named export)\n- `Parser.Language` → `Language` (named export)\n- `language.query(src)` → `new Query(language, src)`\n- `Parser.Language.load()` → `Language.load()`\n\n### GraphView (Sigma.js)\n\n- Graph built once from data; Sigma `nodeReducer`/`edgeReducer` used for filter/selection/hover changes (no remount)\n- `stateRef`/`dispatchRef` pattern to avoid stale closures in event handlers\n- `suppressNextStage` guard ensures `clickNode` event wins over `clickStage`\n- Camera fly-to uses `renderer.getNodeDisplayData(id)` for normalized coordinates (NOT raw graphology attributes)\n- ForceAtlas2 layout applied synchronously after graph build\n\n### Multi-repo Groups\n\n- Contract kinds: `export`, `route`, `schema`, `event`\n- Cross-repo matching via Reciprocal Rank Fusion (RRF)\n- Confidence scoring for cross-repo links\n\n### Build System\n\n- Core: `tsup` bundler → `dist/cli/main.js` + `dist/index.js`\n- Web: Vite + Tailwind CSS v4\n- `esbuild` and `vite` must be in root `devDependencies` to be hoisted for monorepo npm workspaces\n\n---\n\n## 🚢 CI/CD\n\n### GitHub Actions Workflows\n\n| Workflow | Trigger | Steps |\n|----------|---------|-------|\n| **test.yml** | PRs | `npm ci` + `npm test` |\n| **quality.yml** | PRs | Typecheck shared + core + web |\n| **publish.yml** | `v*.*.*` tags | Typecheck → Test → npm audit → License gate → Build core → Build web → `npm publish --provenance` → Build + push multi-arch Docker (linux/amd64 + linux/arm64) → Trivy CRITICAL CVE gate → cosign keyless sign → GitHub Release with CycloneDX SBOM → Discord notification |\n\n### Publishing a New Version\n\n```bash\n# Bump version in code-intel/core/package.json, then:\ngit tag v0.1.5\ngit push origin v0.1.5\n```\n\nThe publish workflow automatically runs all checks, builds the packages, publishes to npm, and sends a Discord notification (📦 success or ❌ failure).\n\n**Required GitHub Secrets:**\n\n| Secret | Purpose |\n|--------|---------|\n| `NPM_TOKEN` | npm access token with publish rights |\n| `DISCORD_WEBHOOK` | Discord webhook URL for deploy notifications |\n\n### Local CI Simulation\n\n```bash\ndocker compose -f docker-compose.build.yml build\n```\n\nUses `node:22-bookworm-slim` — the same base image as GitHub Actions.\n\n---\n\n## 📄 License\n\nMIT © 2024\n","readmeFilename":"README.md"}