codebase-memory-mcp

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 AST analysis across all 158 languages, enhanced with Hybrid LSP semantic type resolution 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 43 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 (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. Release archives are signed and checksummed; every distinct extracted member and unpacked UI asset is submitted to VirusTotal, while the downloadable .tar.gz/.zip containers themselves are not. The release notes record the measured engine count and exact 0/N result; publication requires at least 50 decisive engine results with zero malicious and zero suspicious verdicts. All processing happens 100% locally; your code never leaves your machine. Found a security issue? We want to know — see 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 (UI variant) — 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.
• 158 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.
• 43 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 for the complete matrix and manual/UI-only boundaries.
• Built-in graph visualization — 3D interactive UI at localhost:9749 (optional UI binary variant).
• 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):

curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash

With graph visualization UI:

curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash -s -- --ui

Windows (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: --ui (graph visualization), --skip-config (binary only, no agent setup), --dir=<path> (custom location).

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:

   • codebase-memory-mcp-<os>-<arch>.tar.gz (macOS/Linux) or .zip (Windows) — standard
   • codebase-memory-mcp-ui-<os>-<arch>.tar.gz / .zip — with graph visualization

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

   macOS / Linux:

   tar xzf codebase-memory-mcp-*.tar.gz
   ./install.sh
   

   Windows (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.ndjson.

The native install, update, and uninstall commands are the deliberate exception to that conflict rule. Download, verification, and private same-filesystem staging happen first so a bad candidate never disrupts active work. Activation then publishes account-wide maintenance intent, asks the daemon and every temporary local operation to cancel, and waits to a finite deadline for all coordinated CBM processes to exit. It holds the admission and lifetime barriers exclusively while changing the active binary, configuration, PATH, or indexes. New CBM work cannot enter during this window. Activation progress and results are recorded in ${CBM_CACHE_DIR}/logs/activation-events.ndjson, and a successful command tells you to restart open coding-agent sessions so they launch the activated build.

Package-manager setup (npm, PyPI, or Go) verifies and publishes a coherent private cached runtime set. Sidecars are replaced before the executable with per-file atomic renames; an interrupted multi-file publication is detected and repaired on the next launch rather than being described as one crash-atomic filesystem transaction. It does not replace the active native installation and therefore does not stop running CBM sessions. When that cached binary is executed, it still enters the same exact-build admission barrier. The shell and PowerShell installers invoke the verified candidate's native install command, so they do receive the full account-wide activation guarantee.

The ordinary cli mode is intentionally separate: it runs one command locally and never starts or connects to the coordination daemon, registers a daemon session, or starts watchers/UI. Its only shared state is the OS admission barrier plus per-project locks for graph mutations. While the command is running, a temporary monitor lets activation cancel that operation and its supervised worker safely; the monitor exits with the command and never becomes a standing daemon. See CLI Mode for details.

Graph Visualization UI

The UI currently ships as a separate ui build whose executable embeds only a content-addressed manifest; the deterministic frontend pack is a verified sidecar beside it. The default install on every channel is the lean, headless server; opt into the UI build with:

• install.sh: add --ui (see [Qu