codebase-memory-mcp

# codebase-memory-mcp

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[![arXiv](https://img.shields.io/badge/arXiv-2603.27277-b31b1b?logo=arxiv)](https://arxiv.org/abs/2603.27277)

**The fastest and most efficient code intelligence engine for AI coding agents.** Full-indexes an average repository in milliseconds, the Linux kernel (28M LOC, 75K files) in 3 minutes. Answers structural queries in under 1ms. Ships as a native executable with a small verified runtime-asset set for macOS, Linux, and Windows — download, run `install`, done.

High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across all 162 languages, enhanced with [**Hybrid LSP** semantic type resolution](#hybrid-lsp) for Python, TypeScript / JavaScript / JSX / TSX, PHP, C#, Go, C, C++, Java, Kotlin, Rust, and Perl — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 15 MCP tools. No language runtime, hosted service, or API key. Plug and play across 45 supported automatic/conditional client surfaces.

> **Research** — The design and benchmarks behind this project are described in the preprint [*Codebase-Memory: Tree-Sitter-Based Knowledge Graphs for LLM Code Exploration via MCP*](https://arxiv.org/abs/2603.27277) (arXiv:2603.27277). Evaluated across 31 real-world repositories: 83% answer quality, 10× fewer tokens, 2.1× fewer tool calls vs. file-by-file exploration.

> **Security & Trust** — This tool reads your codebase and writes to your agent configuration files. That is what it is designed to do. If you prefer to audit before running, the [full source is here](https://github.com/DeusData/codebase-memory-mcp). For each release product, three behaviourally identical executable candidates (unstripped, debug-stripped, stripped) are submitted to VirusTotal before testing; the selected candidate is then packaged with its SHA-256 unchanged. Release notes link every measured candidate result. Publication permits only the narrowly documented single-Microsoft `!ml` tolerance in [SECURITY.md](SECURITY.md#our-release-policy). All processing happens 100% locally; your code never leaves your machine. Found a security issue? We want to know — see [SECURITY.md](SECURITY.md). Security is Priority #1 for us.

<p align="center">
  <img src="docs/graph-ui-screenshot.png" alt="Graph visualization UI showing the codebase-memory-mcp knowledge graph" width="800">
  <br>
  <em>Built-in 3D graph visualization — explore your knowledge graph at localhost:9749</em>
</p>

## Why codebase-memory-mcp

- **Extreme indexing speed** — Linux kernel (28M LOC, 75K files) in 3 minutes. RAM-first pipeline: LZ4 compression, in-memory SQLite, fused Aho-Corasick pattern matching. Memory released after indexing.
- **Plug and play** — native executable plus authenticated release-owned assets for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (amd64). The native install needs no Docker, language runtime, or API keys. Download → `install` → restart agent → done.
- **162 languages** — vendored tree-sitter grammars compiled into the binary. Nothing to install, nothing that breaks.
- **120x fewer tokens** — 5 structural queries: ~3,400 tokens vs ~412,000 via file-by-file search. One graph query replaces dozens of grep/read cycles.
- **45 supported automatic/conditional client surfaces** — `install` configures detected clients and safely activates conditional clients only when their documented platform, marker, or explicit existing config path is present. See [Multi-Agent Support](#multi-agent-support) for the complete matrix and manual/UI-only boundaries.
- **Built-in graph visualization** — 3D interactive UI at `localhost:9749`, served from the binary itself.
- **Infrastructure-as-code indexing** — Dockerfiles, Kubernetes manifests, and Kustomize overlays indexed as graph nodes with cross-references. `Resource` nodes for K8s kinds, `Module` nodes for Kustomize overlays with `IMPORTS` edges to referenced resources.
- **15 MCP tools** — search, trace, architecture, impact analysis, targeted index-coverage checks, Cypher queries, dead code detection, cross-service HTTP linking, ADR management, and more.

## Quick Start

**One-line install** (macOS / Linux):
```bash
curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash
```

With graph visualization UI:
```bash
curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash
```

**Windows** (PowerShell):
```powershell
# 1. Download the installer
Invoke-WebRequest -Uri https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.ps1 -OutFile install.ps1

# 2. (Optional but recommended) Inspect the script
notepad install.ps1

# 3. Unblock the downloaded file (removes Mark-of-the-Web restriction added by browsers/Invoke-WebRequest)
Unblock-File .\install.ps1

# 4. Run it
.\install.ps1

```

> **Note:** If you see a script execution policy error, run `Set-ExecutionPolicy -Scope Process Bypass` first, or invoke with `PowerShell -ExecutionPolicy Bypass -File .\install.ps1`.

Options: `--skip-config` (binary only, no agent setup), `--dir=<path>` (custom location).

> **Antivirus note:** Microsoft Defender may flag a release binary as
> `Trojan:Script/Wacatac.B!ml`. This is a known false positive — typically 61 of
> ~62 engines return clean, and the same detection family hits `gh`, llama.cpp,
> Godot and Microsoft's own Go toolchain. See
> [Antivirus False Positives](SECURITY.md#antivirus-false-positives) for the
> evidence, how to verify the artifacts yourself, and how to report it if you
> think we are wrong.

Restart your coding agent. Say **"Index this project"** — done.

<details>
<summary>Manual install</summary>

1. **Download** the archive for your platform from the [latest release](https://github.com/DeusData/codebase-memory-mcp/releases/latest):
   - `codebase-memory-mcp-<os>-<arch>.tar.gz` (macOS/Linux) or `.zip` (Windows)

2. **Extract and install** (each archive includes `install.sh` or `install.ps1`):

   macOS / Linux:
   ```bash
   tar xzf codebase-memory-mcp-*.tar.gz
   ./install.sh
   ```

   Windows (PowerShell):
   ```powershell
   Expand-Archive codebase-memory-mcp-windows-amd64.zip -DestinationPath .
   Unblock-File .\install.ps1
   .\install.ps1
   ```

3. **Restart** your coding agent.

The `install` command automatically strips macOS quarantine attributes and ad-hoc signs the binary — no manual `xattr`/`codesign` needed.
</details>

The `install` command auto-detects installed coding agents and configures their documented MCP entries plus durable instructions, skills, and lifecycle hooks where supported.

### Session Coordination Daemon

CBM automatically shares one per-account coordination daemon across Claude Code, Codex, OpenCode, and every other configured client. There is no opt-in setting for MCP servers or hook clients: the first daemon-backed CBM session starts it, each session registers its own work, and the final session shuts it down. The daemon owns long-lived background services such as watchers, shared indexing jobs, and the optional UI. Closing one session cancels work owned only by that session, while work still needed by another session continues.

The detached daemon does not depend on an MCP frontend's stderr. It keeps owner-only durable records under the canonical `${CBM_CACHE_DIR}/logs` directory (default `~/.cache/codebase-memory-mcp/logs`):

| File | Contents |
|------|----------|
| `cbm-daemon.log` | Daemon lifecycle, watcher/indexing, UI, resource, and error events. |
| `daemon-conflicts.ndjson` | Exact-build, coordination-ABI, and cache-root admission conflicts. |
| `activation-events.ndjson` | Install/update/uninstall activation progress and outcomes. |

Thin frontends still write immediate startup and session-specific errors to their own stderr; MCP JSON-RPC stdout remains clean.

All active CBM processes must run the exact same version, executable build, coordination ABI, and canonical cache root. Equivalent `CBM_CACHE_DIR` aliases resolve to the same root; a genuinely different root is rejected while any CBM process is active. MCP servers, hooks, one-shot CLI commands, temporary index workers, and the daemon share a crash-safe OS admission barrier; starting an ordinary conflicting process fails before doing work and records an explicit conflict in `${CBM_CACHE_DIR}/logs/daemon-conflicts.nd