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Context Manager MCP Server & CLI wrapper using npx","maintainers":[{"name":"senoldogann","email":"contact@senoldogan.dev"}],"readme":"# @senoldogann/context-manager\n\n> 🧠 The Neural Backbone for Autonomous AI Agents\n\n**Node.js wrapper for Cognitive Codebase Matrix (CCM)** - Enables AI agents to understand and navigate your codebase with surgical precision.\n\n**v0.3.13** adds an external benchmark on real repositories (serde, flask,\nexpress) with 35 hand-verified golden tasks and honest Recall@K/MRR/latency\nmetrics — hybrid scoring at 82.9% vs 80.0% semantic-only. **v0.3.12** made the\nbackground semantic upgrade durable (it completes even if the MCP server is\nclosed mid-upgrade) and raised the offline semantic gate to 180/180.\n\n[![npm](https://img.shields.io/npm/v/@senoldogann/context-manager?color=orange)](https://www.npmjs.com/package/@senoldogann/context-manager)\n[![MCP](https://img.shields.io/badge/MCP-Compatible-blue)](https://modelcontextprotocol.io/)\n[![Rust](https://img.shields.io/badge/Built%20With-Rust-orange.svg)](https://www.rust-lang.org/)\n\n---\n\n## 🚀 Quick Start\n\n### Prerequisites\n\n1. **Node.js** 16+ installed\n2. **Ollama** installed and running (for local embeddings)\n   - Download: https://ollama.com\n   - Pull required model: `ollama pull mxbai-embed-large`\n\n### Installation\n\n```bash\n# 1. Install and configure for Codex, Cursor, Claude Desktop, Antigravity, etc.\nnpx @senoldogann/context-manager install\n\n# 2. Index your project\nnpx @senoldogann/context-manager index --path .\n```\n\n**That's it!** Restart your AI editor and start asking questions about your code.\n\n### First-Run Verification\n\nUse this quick smoke test after install:\n\n```bash\n# Verify the CLI responds\nnpx @senoldogann/context-manager query --text \"src/main.rs:1\"\n\n# Verify the MCP binary starts\nnpx @senoldogann/context-manager mcp\n```\n\nIf the wrapper is healthy, the query command should return code context and the MCP process should stay open waiting for stdio messages.\n\nThe first index is complete; subsequent runs are incremental and process only added, changed, renamed, or deleted files. An unchanged project returns a clean no-op.\n\n---\n\n## 📖 What is CCM?\n\nCCM transforms static source code into a dynamic, queryable Knowledge Graph:\n\n- **🔍 Semantic Search** - Find code by meaning (\"where is auth logic?\")\n- **🧠 Graph Navigation** - Understand relationships (\"who calls this function?\")\n- **📍 Cursor Context** - Get relevant code based on your position\n\n---\n\n## 🔧 Commands\n\nThe npm wrapper downloads pre-built binaries and passes commands through:\n\n| Command | Description |\n|---------|-------------|\n| `npx @senoldogann/context-manager install` | Auto-configure MCP for editors |\n| `npx @senoldogann/context-manager index --path <dir>` | Index a project |\n| `npx @senoldogann/context-manager query --text \"...\"` | Search codebase |\n| `npx @senoldogann/context-manager mcp` | Run MCP server directly |\n| `npx @senoldogann/context-manager doctor --path <dir>` | Diagnose config and index health |\n| `npx @senoldogann/context-manager eval --tasks <file>` | Run evaluation tasks |\n| `npx @senoldogann/context-manager learn fixtures` | Generate deterministic synthetic corpus + embedding fixture |\n| `npx @senoldogann/context-manager learn optimize --tasks <file>` | Optimize retrieval policy on train, gate on holdout |\n| `npx @senoldogann/context-manager learn report` | Print Baseline vs Learned report |\n| `npx @senoldogann/context-manager eval --policy <file>` | Evaluate with a specific retrieval policy |\n\nLarge MCP `index_project` runs continue in the server after an early\nacknowledgement. Call `index_project` again to poll for completion instead of\nkeeping one client request open until timeout.\n\n### Supported Hosts\n\n| Host | Status |\n|------|--------|\n| Codex | Supported |\n| Cursor | Supported |\n| Claude Desktop | Supported |\n| Antigravity | Supported |\n\n### Options\n\n```bash\n# Watch mode - auto-reindex on file changes\nnpx @senoldogann/context-manager index --path . --watch\n\n# Custom database path\nnpx @senoldogann/context-manager index --path . --db-path /custom/path\n```\n\n---\n\n## 🔒 Privacy by Default\n\nCCM uses a **Local-First** architecture:\n\n- ✅ Your code **never** leaves your machine\n- ✅ All embeddings run locally via Ollama\n- ✅ No external API calls (unless you configure OpenAI)\n\n---\n\n## ⚙️ Configuration\n\n### Environment Variables\n\nCreate `~/.ccm/.env` (or start from the repository's `.env.example`):\n\n```ini\n# Local (Recommended)\nEMBEDDING_PROVIDER=ollama\nEMBEDDING_HOST=http://127.0.0.1:11434\nEMBEDDING_MODEL=mxbai-embed-large\nEMBEDDING_API_KEY=ollama\n\n# Cloud (Optional)\nEMBEDDING_PROVIDER=openai\nEMBEDDING_API_KEY=sk-your-key\nEMBEDDING_MODEL=text-embedding-3-small\n\n# Networking & Limits\nEMBEDDING_TIMEOUT_SECS=30\nCCM_MAX_FILE_BYTES=2097152\n\n# MCP Security (strict allowlist is ON by default)\nCCM_ALLOWED_ROOTS=/Users/you/projects:/Users/you/sandbox\nCCM_REQUIRE_ALLOWED_ROOTS=1\n\n# MCP Runtime\nCCM_MCP_ENGINE_CACHE_SIZE=8\nCCM_MCP_DEBUG=0\n\n# Optional: disable embeddings entirely (semantic search disabled)\nCCM_DISABLE_EMBEDDER=0\n\n# Optional: embed data files (md/json/yaml) into vector search\nCCM_EMBED_DATA_FILES=0\n\n# Binary checksum verification (0 = enforce, 1 = bypass)\nCCM_ALLOW_UNVERIFIED_BINARIES=0\n\n# Optional binary download tuning\nCCM_DOWNLOAD_TIMEOUT_MS=120000\nCCM_DOWNLOAD_ATTEMPTS=3\n```\n\nAdvanced overrides:\n- `CCM_PROJECT_ROOT` pins the default project root used by the wrapper and MCP fallback engine.\n- `CCM_DB_PATH` overrides the default MCP vector DB location.\n- `.env.example` in the repository contains chunking, batch-size, hybrid-weight, and compatibility-alias settings such as `OPENAI_API_KEY`, `CCM_SKIP_CHECKSUM`, `CCM_MCP_REQUIRE_ALLOWED_ROOTS`, `CCM_EMBED_DATA`, and `EMBEDDING_DISABLED`.\n- Hybrid scoring defaults and tuning notes live in [`docs/hybrid-ranking.md`](https://github.com/senoldogann/LLM-Context-Manager/blob/main/docs/hybrid-ranking.md).\n\n**Security:** The installer writes a strict allowlist into every MCP config (`CCM_PROJECT_ROOT`, `CCM_ALLOWED_ROOTS`, `CCM_REQUIRE_ALLOWED_ROOTS=1`), and the MCP server itself defaults to strict mode. Widen `CCM_ALLOWED_ROOTS` only when you need access to more project roots.\n\n---\n\n## 🤖 Usage in AI\n\nOnce configured, ask your AI agent:\n\n> \"Search for the authentication flow in this codebase.\"\n\n> \"Read the graph for `UserService` and show me its callers.\"\n\n> \"What functions call `parse_config`?\"\n\n## 🧠 Self-Improving Retrieval (v0.3.2+)\n\nCCM can learn a better retrieval policy from experience and prove it on a\nholdout set before activating it:\n\n```bash\n# 1. Generate the deterministic synthetic corpus (repo_a=train, repo_b=holdout)\nnpx @senoldogann/context-manager learn fixtures\n\n# 2. Optimize on train, gate on holdout (Rejected is a valid scientific result)\nCCM_EMBEDDING_FIXTURE=eval/fixtures/embeddings.ndjson \\\n  npx @senoldogann/context-manager learn optimize --seed 42\n\n# 3. Read the Baseline vs Learned report\nnpx @senoldogann/context-manager learn report\n```\n\n- Policies and history live under `data/ccm_learn/` (`policies.json`,\n  `history.jsonl`); the evaluator is immutable during optimization.\n- `CCM_EMBEDDING_FIXTURE` enables offline hybrid evaluation without an embedder.\n- `CCM_TRAJECTORY_LOG=1` records observable retrieval events to\n  `data/ccm_learn/experiences.jsonl` (off by default).\n\n---\n\n## 📦 For Developers\n\nThis package handles:\n\n1. OS/architecture detection\n2. Resumable, retrying compressed binary download from GitHub Releases\n3. Global persistence in `~/.ccm`\n\nAfter the GitHub release workflow succeeds, publish its reviewed npm artifact:\n\n```bash\nVERSION=$(node -p \"require('./package.json').version\")\ngh release download \"v${VERSION}\" \\\n  --pattern \"senoldogann-context-manager-${VERSION}.tgz\" \\\n  --dir .\nnpm publish \"./senoldogann-context-manager-${VERSION}.tgz\" --access public\n```\n\nRunning `npm publish` from the repository root fails because the root intentionally has no `package.json`.\n\n### ✅ Release Reliability\n\n- GitHub Releases publish platform binaries plus `checksums.txt`\n- The npm wrapper verifies checksums before using downloaded binaries\n- Interrupted downloads resume from their partial file and use a bounded timeout/retry policy\n- Redirects are restricted to approved GitHub release hosts\n- Release builds run for Linux, macOS, and Windows before assets are attached\n- Codex configuration is updated directly and atomically, even when the `codex` wrapper is broken\n- The same smoke path is documented here and in the main repository README\n\n### ✅ Binary Integrity\n\nDownloads are verified against `checksums.txt` from the GitHub Release.  \nIf the manifest is missing or a mismatch occurs, you can set `CCM_ALLOW_UNVERIFIED_BINARIES=1` to bypass verification (not recommended).\n\n### 📄 Data Files in Search\n\nBy default, data files (`.md`, `.json`, `.yaml`) are indexed but not embedded.  \nEnable `CCM_EMBED_DATA_FILES=1` to include them in semantic search.\n\n**Source:** https://github.com/senoldogann/LLM-Context-Manager\n\n**Docs:** [English README](https://github.com/senoldogann/LLM-Context-Manager/blob/main/README.md) | [Turkish README](https://github.com/senoldogann/LLM-Context-Manager/blob/main/README.tr.md)\n\n---\n\n## 📝 Changelog\n\n### v0.3.13\n- ✅ New `benchmarks/` suite: 35 hand-verified golden tasks across 3 real\n  open-source repos (serde, flask, express) pinned to exact commits, indexed\n  with real Ollama embeddings\n- ✅ `evaluate_with_mode` emits `ranked` hit lists and per-task `latency_ms` for\n  all query types, enabling Recall@K / MRR@K computation\n- ✅ Honest first results: hybrid 82.9% (29/35) vs semantic-only 80.0% (28/35);\n  `get_context`/`read_graph` 11/11 across all three repos\n\n### v0.3.12\n- ✅ Offline semantic gate raised to **180/180** (100%); the CI gate now requires\n  100% with no regression, and all 50 `search_code` tasks pass\n- ✅ Synthetic fixture embeds at 512 dimensions (was 64), weighting the code\n  symbol ahead of body noise to fix low-dimensional `search_code` recall loss\n- ✅ `score_hits` honors both `node_ids` and `file_paths` when a task supplies both\n- ✅ Background semantic upgrade is **durable**: it runs in a detached OS process\n  group, so it completes even if the MCP server is closed mid-upgrade; failed or\n  interrupted upgrades self-repair on the next `index_project`\n\n### v0.3.11\n- ✅ MCP `index_project` accepts `mode:\"quick\"`; sources are scanned, parsed and\n  graph-referenced immediately while embeddings run in the background\n- ✅ New synchronous `index_now` tool returns final index statistics in one call\n  (`quick`, `full`, `upgrade` modes)\n- ✅ Hybrid `search_code` ranking uses semantic score to break graph-score ties\n- ✅ `update_index` detects a graph-only or incomplete vector table and repairs it\n  from the active graph when no source files changed\n\n### v0.3.10\n- ✅ Embedding security: repo `.env` can no longer override `EMBEDDING_HOST`/API\n  keys; remote embedding hosts require explicit `CCM_ALLOW_REMOTE_EMBEDDING=1`\n- ✅ Path safety: symlinked `data` dirs cannot write artifacts outside the project\n  root; resolved paths are verified inside the canonical project root\n- ✅ Fake call edges from doc comments/strings eliminated; ambiguous stable node\n  IDs rejected instead of mismatched\n- ✅ Policy files written `0600`; parallel corpus eval race fixed\n\n### v0.3.9\n- ✅ Swift symbol names are no longer stolen by attributes (`@MainActor`/`@objc`);\n  `find_nodes`, `get_context` and `impact_of_change` return correct symbols\n- ✅ Real call edges established: self-references no longer block cross-file\n  targets; ambiguous edges traced by `find_usages`/`trace_call_chain`\n- ✅ Full re-index parses files in parallel (rayon); embeddings batched with\n  `CCM_EMBED_CONCURRENCY`\n- ✅ OpenAI-compatible providers extended: HuggingFace TEI, Voyage, Jina, LM\n  Studio, LocalAI, llama.cpp server and Azure OpenAI\n- ✅ Index/manifest/trajectory/policy files written `0600` on Unix; MCP input\n  errors classified as `-32602`\n\n### v0.3.8\n- ✅ Failed scans, parses, embeddings, and full rebuilds preserve the last healthy index\n- ✅ Large MCP indexing is polled in the background while retrieval fails fast during updates\n- ✅ JSON-RPC framing, notifications, discovery calls, allowlists, and corrupt graphs fail safely\n- ✅ Cached npm binaries are checksum-verified and concurrent cold starts use isolated downloads\n\n### v0.3.7\n- ✅ Codex discovery calls `resources/list` and `resources/templates/list` return valid empty lists\n- ✅ `install` updates the canonical agent `SKILL.md` together with MCP configuration\n\n### v0.3.6\n- ✅ npm, Rust crates, GitHub tag and binary assets share one version\n- ✅ Canonical `SKILL.md` is included in the npm tarball\n- ✅ Incomplete LanceDB indexes trigger a full rebuild instead of silent empty search\n- ✅ `read_graph` honors `include_body` and `max_chars`\n- ✅ Release workflow rejects version skew and attaches a verified npm tarball to the GitHub release\n\n### v0.3.5\n- ✅ npm README now documents the v0.3.4 Rust release (offline semantic gate\n  completeness)\n\n### v0.3.4\n- ✅ Offline semantic gate now scores all four query types (`search_code`,\n  `get_context`, `read_graph`, `predict_context`); no more skipped tasks\n- ✅ Rust workspace bumped to 0.3.4\n\n### v0.3.3\n- ✅ Metadata-first MCP output: `include_body`/`max_chars` opt-in snippets, server-side limit cap\n- ✅ Promoted retrieval policy wired into runtime (`PolicyStore::active`)\n- ✅ Eval hybrid ranking aligned with production; per-repo graph cache\n- ✅ `search_code` chunk dedup; parent-pointer BFS for call chains\n- ✅ OpenAI embedder retry; fuzzy stable-id drift resolution\n- ✅ Trajectory records real latency/tool/request id\n- ✅ MCP index writes serialized per project; JSON-RPC id/error fixes\n- ✅ CodeQL analyzes Rust; CI protoc hardened; fixture determinism enforced\n\n### v0.3.2\n- ✅ Versioned `RetrievalPolicy` + `PolicyStore` + history\n- ✅ Deterministic train/holdout splitter and promotion gate (sign test, token guard)\n- ✅ Seeded optimizer: 52 grid candidates + top-3 hill-climb\n- ✅ Offline hybrid eval via `CCM_EMBEDDING_FIXTURE`\n- ✅ `ccm-cli learn {fixtures,optimize,report}` + `eval --policy`\n- ✅ Deterministic synthetic corpus (180 tasks, cross-repo holdout)\n\n### v0.2.1\n- ✅ UTF-8-safe semantic chunking prevents panics on Turkish, Finnish, and emoji content\n- ✅ Cross-file imports, constructors, and type annotations contribute to usage and impact analysis\n- ✅ `get_context` returns the enclosing function/class instead of only a leaf assignment\n- ✅ Incremental `diff_context` includes staged, unstaged, and untracked worktree files\n- ✅ Compressed release binaries, download resume/retry/timeout, Linux ARM64 detection\n- ✅ Codex MCP entries are repaired and enabled without depending on the Codex CLI binary\n- ✅ Release tags run tests, lint, npm tests, indexing, and golden tasks v3 before publishing assets\n\n### v0.1.31\n- ✅ `index_project` is idempotent again and ignores CCM's own generated index files\n- ✅ `search_code` falls back cleanly when embeddings are disabled\n- ✅ Added a real-world Guardian MCP end-to-end test for all 9 tools\n\n### v0.1.27\n- ✅ `search_code` now returns node IDs and location metadata, with configurable limits\n- ✅ New `find_nodes` MCP tool for graph node discovery before `read_graph`\n- ✅ `index_project` now reports clean no-op refreshes and ignores internal CCM index files\n\n### v0.1.26\n- ✅ Trusted publishing workflow updated for modern Node and npm requirements\n- ✅ Release jobs now skip npm publish when the same version is already live\n- ✅ Safer wrapper binary downloads during concurrent first-run installs\n\n### v0.1.25\n- ✅ npm publish now uses GitHub Actions trusted publishing (OIDC)\n- ✅ Clearer first-run verification and release reliability docs\n\n### v0.1.24\n- ✅ Native `protoc` installation in GitHub Actions release builds\n- ✅ Updated release workflow actions for newer runner compatibility\n\n### v0.1.23\n- ✅ JSON-RPC request size limit for safer MCP stdio transport\n- ✅ Sensitive value redaction in MCP debug logs\n- ✅ Hardened path normalization for MCP graph and context tools\n- ✅ GitHub release redirect allowlist for binary downloads\n- ✅ Unused core dependency cleanup\n\n### v0.1.22\n- ✅ Codex installer support via `codex mcp add`\n- ✅ Cursor config support via `~/.cursor/mcp.json`\n- ✅ Evaluation bootstraps missing indexes before scoring\n- ✅ Golden tasks refreshed for the current repo layout\n\n### v0.1.21\n- ✅ Release checksums (`checksums.txt`) for binary integrity\n- ✅ MCP allowlist with optional strict enforcement\n- ✅ Data file embedding is optional (`CCM_EMBED_DATA_FILES`)\n- ✅ CLI/MCP integration tests\n\n### v0.1.20\n- ✅ 100% evaluation pass rate\n- ✅ Hybrid scoring (graph + semantic)\n- ✅ Lazy indexing support\n- ✅ Watch mode for auto-reindexing\n\n---\n\nBuilt with ❤️ in **Rust**\n","readmeFilename":"README.md"}