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 single static binary 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. Zero dependencies. 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 — every release binary is signed, checksummed, and scanned by 70+ antivirus engines. 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.

Built-in 3D graph visualization (UI variant) — explore your knowledge graph at localhost:9749

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 — single static binary for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (amd64). No Docker, no runtime dependencies, no 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.

Manual install

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

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

Restart your coding agent.

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

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

Graph Visualization UI

The UI ships as a separate ui build (it embeds the frontend). The default install on every channel is the lean, headless server; opt into the UI build with:

install.sh: add --ui (see Quick Start)
npm: CBM_VARIANT=ui npm install -g codebase-memory-mcp
PyPI: CBM_VARIANT=ui pip install codebase-memory-mcp
Manual: download the codebase-memory-mcp-ui-<os>-<arch> archive

Then run it:

codebase-memory-mcp --ui=true --port=9749

Open http://localhost:9749 in your browser. The UI runs as a background thread alongside the MCP server — it's available whenever your agent is connected.

Auto-Index

Enable automatic indexing on MCP session start:

codebase-memory-mcp config set auto_index true

When enabled, new projects are indexed automatically on first connection. Previously-indexed projects are registered with the background watcher for ongoing git-based change detection. Configurable file limit: config set auto_index_limit 50000.

Watcher registration is controlled separately by auto_watch (default true). Set config set auto_watch false to keep a session from registering its project with the background watcher — useful when working across many projects and you want each session contained to explicit indexing.

Keeping Up to Date

codebase-memory-mcp update

The MCP server also checks for updates on startup and notifies on the first tool call if a newer release is available.

Uninstall

codebase-memory-mcp uninstall

Removes owned agent config entries, skills, hooks, instructions, and the installed binary. Existing graph indexes are listed and deleted only after confirmation.

Features

Graph & analysis

Architecture overview: get_architecture returns languages, packages, entry points, routes, hotspots, boundaries, layers, and clusters in a single call
Architecture Decision Records: manage_adr persists architectural decisions across sessions
Louvain community detection: Discovers functional modules by clustering call edges
Git diff impact mapping: detect_changes maps uncommitted changes to affected symbols with risk classification
Call graph: Resolves function calls across files and packages (import-aware, type-inferred)
Dead code detection: Finds functions with zero callers, excluding entry points
Cypher-like queries: MATCH (f:Function)-[:CALLS]->(g) WHERE f.name = 'main' RETURN g.name

Search

Semantic search (semantic_query): vector search across the entire graph, powered by bundled Nomic nomic-embed-code embeddings (40K tokens, 768d int8) compiled into the binary — no API key, no Ollama, no Docker. 11-signal combined scoring (TF-IDF, RRI, API/Type/Decorator signatures, AST profiles, data flow, Halstead-lite, MinHash, module proximity, graph diffusion).
BM25 full-text search via SQLite FTS5 with cbm_camel_split tokenizer (camelCase / snake_case aware)
Structural search (search_graph): regex name patterns, label filters, min/max degree, file scoping
Code search (search_code): graph-augmented grep over indexed files only

Cross-service linking

HTTP route ↔ call-site matching with confidence scoring
gRPC, GraphQL, tRPC service detection with protobuf Route extraction
Channel detection (EMITS / LISTENS_ON) for Socket.IO, EventEmitter, and generic pub-sub patterns across 8 languages with constant resolution

Cross-repo intelligence

CROSS_* edges link nodes across multiple repos indexed under the same store
Multi-galaxy 3D UI layout for cross-repo architecture visualization
Cross-repo architecture summary combining services, routes, and dependencies across the indexed fleet

Edge types (selected)

CALLS, IMPORTS, DEFINES, IMPLEMENTS, INHERITS
HTTP_CALLS, ASYNC_CALLS (cross-service)
EMITS, LISTENS_ON (channels)
DATA_FLOWS with arg-to-param mapping + field access chains
SIMILAR_TO (MinHash + LSH near-clone detection, Jaccard scored)
SEMANTICALLY_RELATED (vocabulary-mismatch, same-language, score ≥ 0.80)

Indexing pipeline

158 vendored tree-sitter grammars compiled into the binary
Generic package / module resolution — bare specifiers like @myorg/pkg, github.com/foo/bar, use my_crate::foo resolved via manifest scanning (package.json, go.mod, Cargo.toml, pyproject.toml, composer.json, pubspec.yaml, pom.xml, build.gradle, mix.exs, *.gemspec)
Infrastructure-as-code indexing — Dockerfiles, Kubernetes manifests, Kustomize overlays as graph nodes
Hybrid LSP semantic type resolution for Python, TypeScript / JavaScript / JSX / TSX, PHP, C#, Go, C, C++, Java, Kotlin, Rust, and Perl — a lightweight C implementation of language type-resolution algorithms, structurally inspired by and compatible with major language servers including tsserver / typescript-go, pyright, gopls, Roslyn, Eclipse JDT, and rust-analyzer (parameter binding, return-type inference, generic substitution, JSX component dispatch, JSDoc inference for plain JS files, namespace + trait + late-static-binding resolution for PHP, file-scoped namespaces + records + LINQ method syntax for C#, class-hierarchy + overload + lambda resolution for Java, extension-function + scope-function resolution for Kotlin, trait-method + UFCS resolution for Rust)
RAM-first pipeline: LZ4 compression, in-memory SQLite, single dump at end. Memory released after.

Distribution & operation

Single static binary, zero infrastructure: SQLite-backed, persists to ~/.cache/codebase-memory-mcp/
Auto-sync: Background watcher detects file changes and re-indexes automatically
Route nodes: REST endpoints are first-class graph entities
CLI mode: codebase-memory-mcp cli search_graph '{"project": "my-project", "name_pattern": ".*Handler.*"}'
Available on: npm, PyPI, Homebrew, Scoop, Winget, Chocolatey, AUR, go install

Team-Shared Graph Artifact

Commit a single compressed file to your repo and your teammates skip the reindex.

.codebase-memory/graph.db.zst is a zstd-compressed snapshot of the knowledge graph that lives next to your source. When you index, the artifact is written or refreshed; when a teammate clones the repo and runs codebase-memory-mcp for the first time, the artifact is decompressed and incremental indexing fills in their local diff.

Format: SQLite database, indexes stripped, VACUUM INTO compacted, then zstd 1.5.7 compressed (8–13:1 ratio typical)
Two tiers:
- Best (zstd -9 + index strip + VACUUM INTO) — written on explicit index_repository
- Fast (zstd -3) — written by the watcher for low-latency incremental updates
Bootstrap: when no local DB exists but the artifact is present, index_repository imports the artifact first, then runs incremental indexing — avoiding the full reindex cost
No merge pain: a .gitattributes line with merge=ours is auto-created on first export, so concurrent edits don't produce conflicts on the binary artifact
Optional: never committed unless you want it. Add .codebase-memory/ to .gitignore if you prefer everyone to reindex from scratch.

The result is similar in spirit to graphify's graphify-out/ directory, but as a single compressed file with explicit two-tier export, integrity-checked import, and zero merge friction.

How It Works

codebase-memory-mcp is a structural analysis backend — it builds and queries the knowledge graph. It does not include an LLM. Instead, it relies on your MCP client (Claude Code, or any MCP-compatible agent) to be the intelligence layer.

You: "what calls ProcessOrder?"

Agent calls: trace_path(function_name="ProcessOrder", direction="inbound")

codebase-memory-mcp: executes graph query, returns structured results

Agent: presents the call chain in plain English

Why no built-in LLM? Other code graph tools embed an LLM for natural language → graph query translation. This means extra API keys, extra cost, and another model to configure. With MCP, the agent you're already talking to is the query translator.

Performance

Benchmarked on Apple M3 Pro:

Operation	Time	Notes
Linux kernel full index	3 min	28M LOC, 75K files → 4.81M nodes, 7.72M edges
Linux kernel fast index	1m 12s	1.88M nodes
Django full index	~6s	49K nodes, 196K edges
Cypher query	<1ms	Relationship traversal
Name search (regex)	<10ms	SQL LIKE pre-filtering
Dead code detection	~150ms	Full graph scan with degree filtering
Trace call path (depth=5)	<10ms	BFS traversal

RAM-first pipeline: All indexing runs in memory (LZ4 HC compressed read, in-memory SQLite, single dump at end). Memory is released back to the OS after indexing completes.

Token efficiency: Five structural queries consumed ~3,400 tokens via codebase-memory-mcp versus ~412,000 tokens via file-by-file grep exploration — a 99.2% reduction.

Troubleshooting & Diagnostics

codebase-memory-mcp runs 100% locally and collects no telemetry — your code, queries, environment, and usage never leave your machine. That privacy guarantee also means that when you hit something we can't reproduce on our side (a slow memory climb over hours, a performance regression, a leak that only appears after days of real use), we have no data at all unless you choose to send it. Here is how to capture it yourself.

Capture a diagnostics log

Set CBM_DIAGNOSTICS=1 before the MCP server starts, then reproduce the problem (let it run as long as it takes — a slow leak needs time to show in the trend). The server writes two files to your system temp directory ($TMPDIR or /tmp on macOS/Linux, %TEMP% on Windows):

File	What it is
`cbm-diagnostics-<pid>.ndjson`	The memory trajectory — one JSON line every 5 s with `rss`, `committed` (Windows commit charge), `peak_`, `page_faults`, `fd`, and `queries`. This is the file we need for memory/leak reports* — the trend over time is what pinpoints a leak. It is kept on disk after the server exits (so you can grab it post-mortem) and rotates to `.ndjson.1` past ~8 MB.
`cbm-diagnostics-<pid>.json`	The latest snapshot only — handy for a quick live check. Removed on clean exit.

The startup log prints both paths, e.g.:

level=info msg=diagnostics.start snapshot=/tmp/cbm-diagnostics-12345.json trajectory=/tmp/cbm-diagnostics-12345.ndjson interval=5s

Set the variable in the env block of your agent's MCP server config, or export it before launching the server.

What to share

When you open a memory/performance issue, attach the .ndjson trajectory — it contains no source code or query text, only resource counters. If you'd rather not attach a file, paste it (or an agent's summary of it) into the issue: your assistant can read the NDJSON directly and report whether rss/committed grow monotonically, how fast, and relative to query count — which is exactly what we need to find the cause.

Installation

Pre-built Binaries

Platform	Standard	With Graph UI
macOS (Apple Silicon)	`codebase-memory-mcp-darwin-arm64.tar.gz`	`codebase-memory-mcp-ui-darwin-arm64.tar.gz`
macOS (Intel)	`codebase-memory-mcp-darwin-amd64.tar.gz`	`codebase-memory-mcp-ui-darwin-amd64.tar.gz`
Linux (x86_64)	`codebase-memory-mcp-linux-amd64.tar.gz`	`codebase-memory-mcp-ui-linux-amd64.tar.gz`
Linux (ARM64)	`codebase-memory-mcp-linux-arm64.tar.gz`	`codebase-memory-mcp-ui-linux-arm64.tar.gz`
Windows (x86_64)	`codebase-memory-mcp-windows-amd64.zip`	`codebase-memory-mcp-ui-windows-amd64.zip`

Every release includes checksums.txt with SHA-256 hashes. All binaries are statically linked — no shared library dependencies.

Windows note: SmartScreen may show a warning for unsigned software. Click "More info" → "Run anyway". Verify integrity with checksums.txt.

Setup Scripts

Automated download + install

macOS / Linux:

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

Windows (PowerShell):

irm https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/scripts/setup-windows.ps1 | iex

AUR (Arch Linux)

yay -S codebase-memory-mcp-bin

paru -S codebase-memory-mcp-bin

The codebase-memory-mcp-bin package is available at: https://aur.archlinux.org/packages/codebase-memory-mcp-bin

Install via Claude Code

You: "Install this MCP server: https://github.com/DeusData/codebase-memory-mcp"

Build from Source

Prerequisites: C compiler + zlib

Requirement	Check	Install
C compiler (gcc or clang)	`gcc --version` or `clang --version`	macOS: `xcode-select --install`, Linux: `apt install build-essential`
C++ compiler	`g++ --version` or `clang++ --version`	Same as above
zlib	—	macOS: included, Linux: `apt install zlib1g-dev`
Git	`git --version`	Pre-installed on most systems

git clone https://github.com/DeusData/codebase-memory-mcp.git
cd codebase-memory-mcp
scripts/build.sh                    # standard binary
scripts/build.sh --with-ui          # with graph visualization
# Binary at: build/c/codebase-memory-mcp

Manual MCP Configuration

If you prefer not to use the install command

Add to ~/.claude.json (user scope) or project .mcp.json:

{
  "mcpServers": {
    "codebase-memory-mcp": {
      "command": "/path/to/codebase-memory-mcp",
      "args": []
    }
  }
}

Restart your agent. Verify with /mcp — you should see codebase-memory-mcp with 15 tools.

Multi-Agent Support

install configures 43 client surfaces: 37 detected automatically and 6 conditional or explicit. “Conditional” means the installer writes only when the documented platform or an explicit, already-existing config path proves the target is active. It never flips experimental feature flags, enables plugins, YOLO modes, global permission bypasses, or third-party instruction trust.

Where a client has a documented custom-agent format, the installer creates three exact-owned definitions from one canonical contract:

Scout (Tier 1) — about 3–4 narrow calls for fast positive, provisional discovery; no absence, exhaustive-impact, or dead-code claims.
Verify (Tier 2, default) — task-directed graph evidence, exact source checks, path coverage for every cited file, and scope coverage before negative claims.
Auditor (Tier 3) — bounded scope, current index generation, complete relevant pagination, broader relationship checks, and explicit unresolved limitations.

Every direct tier batches check_index_coverage for its evidence paths and reads flagged ranges or skipped/excluded files directly. A clean coverage result means only “no recorded gap,” never proof of completeness. Clients without safe child MCP access receive the same three tiers as parent-handoff agents; the parent must supply project, generation, pagination state, graph evidence, and coverage results. Updates migrate only byte-identical prior Verify definitions and never overwrite user-modified agents.

Agent	Activation	MCP config	Durable context / augmentation
Claude Code	Detected	`~/.claude.json`	Skill + three exact-tool graph agents; `SessionStart`, `SubagentStart`, non-blocking `PreToolUse` for `Grep`/`Glob`, and post-`Read` coverage
Codex CLI	Detected	`$CODEX_HOME/config.toml`	`AGENTS.md`, skill, three read-only agents; `SessionStart` + `SubagentStart`
Gemini CLI	Detected	`.gemini/settings.json`	`GEMINI.md`, three explicit read/graph-tool subagents; `BeforeTool`, `AfterTool` `read_file` coverage, and `SessionStart`
Zed	Detected	platform `settings.json` (JSONC)	`AGENTS.md` + shared skill
OpenCode	Detected	`$OPENCODE_CONFIG` or resolved global config	`AGENTS.md`, skill, three deny-by-default read-only agents
Antigravity	Detected	`.gemini/config/mcp_config.json`	`.gemini/GEMINI.md`
Aider	Detected	—	`CONVENTIONS.md` via `.aider.conf.yml`
KiloCode	Detected	`.config/kilo/kilo.jsonc`	Rule + three graph-tool subagents with deny-by-default permissions
VS Code	Detected	platform `Code/User/mcp.json`	`~/.copilot/skills`, three read-only agents, `sessionStart` + `subagentStart`
Cursor	Detected	`.cursor/mcp.json`	Skill + three read-only parent-handoff agents; context hooks withheld because session injection races and `readonly` blocks MCP
Windsurf	Detected	`~/.codeium/windsurf/mcp_config.json`	Always-on `global_rules.md`
Augment / Auggie	Detected	`~/.augment/settings.json`	Rule, three read-only handoff subagents, `SessionStart` + post-`view` coverage
OpenClaw	Detected	`$OPENCLAW_CONFIG_PATH` or state `openclaw.json`	Active-workspace `AGENTS.md` + `TOOLS.md`; compaction reinjection
Kiro	Detected	`$KIRO_HOME/settings/mcp.json`	Steering, skill, three JSON agents with isolated Scout/Analysis-profile MCP and explicit graph-tool selectors (`includeMcpJson: false`)
Junie	Detected	`.junie/mcp/mcp.json`	Skill + three graph subagents for EAP-capable builds; Scout and Analysis server aliases hard-limit the tier tool surfaces; no ineffective EAP `SessionStart` hook
Hermes	Detected	`$HERMES_HOME/config.yaml`	Skill + fail-open `pre_llm_call` context augmentation
OpenHands	Detected	`.openhands/mcp.json`	Shared `.agents/skills/codebase-memory/SKILL.md`
Cline	Detected	`~/.cline/mcp.json` + `${CLINE_DATA_DIR:-~/.cline/data}/settings/cline_mcp_settings.json`	Rule + skill; automatic file hooks withheld because they auto-activate and their output is not reliably consumed; child agents cannot use MCP
Warp	Detected, skill only	UI, Warp Drive, or per invocation (manual)	Shared `~/.agents/skills/codebase-memory/SKILL.md`
Qwen Code	Detected	`.qwen/settings.json`	`QWEN.md`, skill, three explicit read/graph-tool agents; `SessionStart`, `SubagentStart`, and post-`ReadFile` coverage
GitHub Copilot CLI	Detected	`$COPILOT_HOME/mcp-config.json`	Instructions, skill, three read-only agents; `sessionStart` + `subagentStart`
Factory Droid	Detected	`.factory/mcp.json`	`AGENTS.md`, skill, three droids with exact per-tier graph-tool lists (without additive whole-server exposure); `SessionStart` + post-`Read` coverage on macOS/Linux, withheld on Windows
Crush	Detected	`.config/crush/crush.json`	Managed context path with explicit parent-to-child handoff
Goose	Detected	`.config/goose/config.yaml`	`.goosehints`
Mistral Vibe	Detected	`$VIBE_HOME/config.toml`	`AGENTS.md`, skill, and three matched agent/prompt pairs with explicit read-only graph-tool allowlists
Qoder CLI	Detected	`~/.qoder/settings.json`	Skill, three directly MCP-attached agents with named-server scoping and exact per-tier graph-tool lists; `SessionStart`, `SubagentStart`, and post-`Read` coverage, including documented PowerShell execution on Windows
Kimi Code CLI	Detected	`$KIMI_CODE_HOME/mcp.json` (default `~/.kimi-code`)	Same-root `AGENTS.md` + skill; fail-open `UserPromptSubmit` hook in `config.toml`
GitLab Duo CLI	Detected	`$GLAB_CONFIG_DIR/duo/mcp.json` or platform fallback	Fail-open user `SessionStart` on macOS/Linux; hook withheld on Windows; no experimental global skill enablement
Rovo Dev CLI	Detected	configured override or `~/.rovodev/mcp.json`	Global `AGENTS.md`, skill + three read-only handoff subagents; no undocumented hook
Amp	Detected	`~/.config/agents/skills/codebase-memory/mcp.json`	Colocated skill + `~/.config/amp/AGENTS.md`; no plugin
Devin CLI / Local	Detected	`~/.config/devin/config.json` (platform app-data path on Windows)	Same-root `AGENTS.md` + skill; macOS/Linux `UserPromptSubmit` + `PostCompaction`, and `SessionStart` only when Claude does not already provide it; hooks withheld on Windows
Tabnine	Detected	`~/.tabnine/mcp_servers.json`	MCP only; no experimental/YOLO setting
Continue / cn	Conditional	Existing `~/.continue/config.yaml` or `$CBM_CONTINUE_CONFIG_PATH`	MCP only
Visual Studio	Conditional, Windows	`~/.mcp.json`	MCP only
TRAE	Conditional	Existing `$CBM_TRAE_CONFIG_PATH`	MCP only
Roo Code	Conditional	Existing `$CBM_ROO_CONFIG_PATH`	MCP only
Amazon Q Developer IDE	Detected	`~/.aws/amazonq/default.json` (preserves an existing `agents/default.json` or legacy `mcp.json`)	MCP only
CodeBuddy Code CLI	Detected	`~/.codebuddy/.mcp.json` (preserves an active deprecated/legacy file)	`CODEBUDDY.md`, skill, three read-only graph agents; beta hooks are not auto-installed
IBM Bob Shell	Detected by `bob`	`~/.bob/mcp_settings.json`	Shared rule; no invented hook or agent
Pochi	Detected	`~/.pochi/config.jsonc` (`mcp`)	`README.pochi.md`, skill, and three `readFile`-only parent-handoff agents
Pi	Detected	—	`~/.pi/agent/AGENTS.md` + skill; MCP/subagents require an explicit reviewed extension
IBM Bob IDE	Conditional	Existing `~/.bob/mcp.json`	Shared rule + IDE skill; no invented hook or agent
Sourcegraph Cody	Explicit opt-in	Existing `$CBM_CODY_CONFIG_PATH`	MCP only

Sessions, compaction, and subagents

Hooks installed by this project are fail-open and context-only. Claude Code's PreToolUse observes Grep/Glob and injects matching graph symbols as additionalContext; PostToolUse on Read adds targeted coverage context when the graph could not fully parse or index that file. It never denies or replaces the requested tool call.

Claude Code, Codex CLI, Qwen Code, GitHub Copilot CLI, and VS Code's Copilot runtime receive paired session/subagent context where the vendor exposes a documented context-output contract. Codex users must review and trust installed hooks through /hooks; changing a hook definition changes its trust hash, so an update can require re-trust. Qoder uses SessionStart, SubagentStart, and post-Read coverage, including its documented PowerShell executor on Windows. Kimi uses UserPromptSubmit, while Hermes uses pre_llm_call; both retain their documented Windows execution paths. Devin installs UserPromptSubmit and PostCompaction on macOS/Linux and adds SessionStart only when Claude's equivalent managed hook is not present. GitLab Duo gets a narrowly scoped macOS/Linux user SessionStart entry on its experimental hook surface. GitLab Duo, Devin, and Factory hooks are withheld on Windows because those vendors do not document a deterministic shell/executor contract there. Gemini CLI, Factory Droid, and Augment also add documented post-read/view coverage context but expose no equivalent documented child-start context.

For runtimes without a stable context-producing lifecycle event, durable files carry the contract across fresh sessions and compaction: verify the graph project and index freshness, query structural facts in the parent, then pass the project, qualified symbols, paths, and call-chain evidence in every delegated task. Claude, Codex, Gemini, Kiro, Qwen, Copilot, CodeBuddy, OpenCode, Kilo, Vibe, Qoder, Junie, and Factory receive Scout, Verify, and Auditor graph profiles. Kiro embeds this MCP server with --tool-profile scout for Scout and --tool-profile analysis for Verify/Auditor. Junie registers equivalent named server aliases because its subagent schema filters by server rather than by individual tool. Both process profiles use positive allowlists: Scout exposes seven fast inspection tools, Analysis exposes eleven, and future or mutating tools remain unavailable until explicitly reviewed. If either Junie alias collides with user configuration, the installer preserves it and installs parent-handoff profiles instead. Qoder combines its documented named-server selection with exact tier-specific MCP tool IDs. Factory uses exact registered MCP tool IDs without its additive mcpServers field, which would expose the whole server. Codex, Kilo, Vibe, and other capable formats likewise enumerate the narrowest supported tool set. Rovo, Cursor, Augment, Pochi, and Cline use parent handoff where direct child MCP is unavailable or unsafe; Pochi is limited to readFile, and Cline child agents cannot use MCP.

Cline's file hooks auto-activate when present, and current Cline does not reliably consume their context output, so automatic adapters are withheld and older owned adapters are cleaned up. CodeBuddy's beta, version-gated hooks are not auto-installed. Junie's EAP SessionStart output is documented as ignored, so no context hook is installed. Junie custom agents remain EAP-dependent. Qoder can resolve higher-priority project or plugin agents before user agents with the same name; reload the client after installation or profile changes. Cursor context hooks are withheld: session context injection has a known race, subagentStart is control-only, and read-only subagents cannot safely receive MCP access. Rovo has no documented session context-output hook, and Bob documents neither a suitable hook nor a custom-agent surface. Those surfaces are not approximated with invented augmentation. Kimi plugins, Amp plugins, and GitLab experimental global skills remain opt-in.

OpenClaw reinjects the Codebase Knowledge Graph (codebase-memory-mcp) AGENTS section after compaction and places the same guidance in TOOLS.md, the bootstrap files inherited by its subagents. Automatic augmentation covers the active/default workspace. Separate agents.list[].workspace directories require making that workspace active for installation or copying the managed block there.

The installed Claude shim is named cbm-code-discovery-gate for backward compatibility; despite the legacy name, it never gates or blocks.

Manual or UI-managed integrations

These are intentionally not counted as automatic installs: Qodo MCP is added through its UI and may be governed by enterprise allowlists; Warp MCP is managed through Warp Drive/UI or per invocation (only the shared skill is automatic); JetBrains AI Assistant / ACP is IDE-managed; GitHub Copilot coding agent, Jules, and CodeRabbit are cloud/repository-managed; Replit exposes a remote/service integration rather than a stable local user-global client; BLACKBOX AI does not document a stable arbitrary user-global MCP/instruction/agent schema; Plandex has no stable global registry safe to mutate; and SWE-agent uses explicit YAML and is no longer a suitable automatic global target.

CLI Mode

Every MCP tool can be invoked from the command line:

codebase-memory-mcp cli index_repository '{"repo_path": "/path/to/repo"}'
codebase-memory-mcp cli list_projects

# Use the "name" returned by list_projects as the project value.
codebase-memory-mcp cli search_graph '{"project": "my-project", "name_pattern": ".*Handler.*", "label": "Function"}'
codebase-memory-mcp cli trace_path '{"project": "my-project", "function_name": "Search", "direction": "both"}'
codebase-memory-mcp cli query_graph '{"project": "my-project", "query": "MATCH (f:Function) RETURN f.name LIMIT 5"}'
codebase-memory-mcp cli --raw search_graph '{"project": "my-project", "label": "Function"}' | jq '.results[].name'

MCP Tools

Indexing

Tool	Description
`index_repository`	Index a repository into the graph. Auto-sync keeps it fresh after that.
`list_projects`	List all indexed projects with node/edge counts.
`delete_project`	Remove a project and all its graph data.
`index_status`	Check indexing status of a project.

Querying

Tool	Description
`search_graph`	Structured search by label, name pattern, file pattern, degree filters. Pagination via limit/offset.
`trace_path`	BFS traversal — who calls a function and what it calls (alias: `trace_call_path`). Depth 1-5.
`detect_changes`	Map git diff to affected symbols + blast radius with risk classification.
`query_graph`	Execute Cypher-like graph queries (read-only).
`get_graph_schema`	Node/edge counts, relationship patterns, property definitions per label. Run this first.
`get_code_snippet`	Read source code for a function by qualified name.
`get_architecture`	Codebase overview: languages, packages, routes, hotspots, clusters, ADR.
`search_code`	Grep-like text search within indexed project files.
`manage_adr`	CRUD for Architecture Decision Records.
`ingest_traces`	Ingest runtime traces to validate HTTP_CALLS edges.

Graph Data Model

Node Labels

Project, Package, Folder, File, Module, Class, Function, Method, Interface, Enum, Type, Route, Resource

Edge Types

CONTAINS_PACKAGE, CONTAINS_FOLDER, CONTAINS_FILE, DEFINES, DEFINES_METHOD, IMPORTS, CALLS, HTTP_CALLS, ASYNC_CALLS, IMPLEMENTS, HANDLES, USAGE, CONFIGURES, WRITES, MEMBER_OF, TESTS, USES_TYPE, FILE_CHANGES_WITH

Qualified Names

get_code_snippet uses qualified names: <project>.<path_parts>.<name>. Use search_graph to discover them first.

Supported Cypher (openCypher read subset)

query_graph is a read-only openCypher subset:

Clauses: MATCH, OPTIONAL MATCH, multiple MATCH, WHERE, WITH (+ WITH … WHERE), RETURN, ORDER BY, SKIP, LIMIT, DISTINCT, UNWIND, UNION / UNION ALL, CASE.
Patterns: labelled nodes, label alternation (n:A|B), relationship types/direction, variable-length paths [*1..3], inline property maps.
WHERE: = <> < <= > >=, AND/OR/XOR/NOT, IN, CONTAINS, STARTS WITH, ENDS WITH, IS [NOT] NULL, regex =~, label test n:Label, and EXISTS { (n)-[:TYPE]->() } (single-hop existence — great for dead-code, e.g. WHERE NOT EXISTS { (f)<-[:CALLS]-() }).
Aggregates: count (+DISTINCT), sum, avg, min, max, collect.
Functions: labels, type, id, keys, properties; toLower/toUpper/toString/toInteger/toFloat/toBoolean; size, length, trim/ltrim/rtrim, reverse; coalesce, substring, replace, left, right.

Anything outside this subset (write/MERGE/CALL clauses, unsupported functions, list/map literals, comprehensions, path functions, parameters) fails with a clear unsupported … error rather than returning empty results.

Ignoring Files

Layered: hardcoded patterns (.git, node_modules, etc.) → .gitignore hierarchy → .cbmignore (project-specific, gitignore syntax). Symlinks are always skipped.

See docs/cbmignore.md for the full .cbmignore how-to: syntax, precedence across the ignore layers, and negation semantics.

Configuration

codebase-memory-mcp config list                          # show all settings
codebase-memory-mcp config set auto_index true           # auto-index on session start
codebase-memory-mcp config set auto_index_limit 50000    # max files for auto-index
codebase-memory-mcp config set auto_watch false          # don't register background git watcher (default: true)
codebase-memory-mcp config reset auto_index              # reset to default

Environment Variables

Variable	Default	Description
`CBM_ALLOWED_ROOT`	(unset)	Restrict `index_repository` to paths within this directory. When set, a `repo_path` that resolves (after symlink / `..` resolution) outside this root is refused; unset imposes no restriction. Useful when the server may be driven by an untrusted caller, e.g. agentic or multi-tenant deployments.
`CBM_CACHE_DIR`	`~/.cache/codebase-memory-mcp`	Override the database storage directory. All project indexes and config are stored here.
`CBM_DIAGNOSTICS`	`false`	Set to `1` or `true` to enable periodic diagnostics output to `/tmp/cbm-diagnostics-<pid>.json`.
`CBM_DOWNLOAD_URL`	(GitHub releases)	Override the download URL for updates. Used for testing or self-hosted deployments.
`CBM_LOG_LEVEL`	`info`	Set the minimum log level. Accepted values (case-insensitive): `debug`, `info`, `warn`, `error`, `none` — or their numeric equivalents `0`–`4` matching the internal enum. Logs go to stderr; stdout is reserved for MCP JSON-RPC.
`CBM_WORKERS`	(detected)	Override the parallel-indexing worker count returned by `cbm_default_worker_count`. Useful inside containers where `sysconf(_SC_NPROCESSORS_ONLN)` reports host CPUs rather than the cgroup's effective quota. Range 1–256; invalid values are ignored with a warning.
`CBM_MEM_BUDGET_MB`	(detected)	Override the in-memory graph budget with an explicit cap in MiB, taking precedence over the `ram_fraction × total_RAM` default. Useful on bare-metal hosts without a cgroup limit, or to pin a budget below the cgroup limit so headroom is left for sibling processes. Must be a positive integer; it is clamped to detected total RAM (logged as `mem.budget.clamped`), and non-numeric or non-positive values are ignored with a warning (`mem.budget.env.invalid`).
`CBM_DUMP_VERIFY_MIN_RATIO`	`0.5`	After indexing, compare persisted SQLite node count to the in-memory dump count. When persisted nodes fall below this fraction of committed nodes (and committed > 50), `index_repository` returns `status:"degraded"` instead of silent `indexed`. Range 0–1; set `0` to disable. Invalid values are ignored with a warning.

# Store indexes in a custom directory
export CBM_CACHE_DIR=~/my-projects/cbm-data

Custom File Extensions

The JSON config files support a single key, extra_extensions, which maps additional file extensions to supported languages. Useful for framework-specific extensions like .blade.php (Laravel) or .mjs (ES modules). (For other tunables, see Environment Variables and the config subcommand above.)

Need the full config-file reference? See docs/CONFIGURATION.md.

Per-project (in your repo root):

// .codebase-memory.json
{"extra_extensions": {".blade.php": "php", ".mjs": "javascript"}}

Global (applies to all projects):

// ~/.config/codebase-memory-mcp/config.json  (or $XDG_CONFIG_HOME/...)
{"extra_extensions": {".twig": "html", ".phtml": "php"}}

Each entry maps an extension (which must start with .) to a language name. Language names are matched case-insensitively. Accepted values (aliases in parentheses) are:

bash (sh), c, c++ (cpp), c# (csharp), clojure, cmake, cobol, common lisp (commonlisp, lisp), css, cuda, dart, dockerfile, elixir, elm, emacs lisp (emacslisp), erlang, f# (fsharp), form, fortran, glsl, go, graphql, groovy, haskell, hcl (terraform), html, ini, java, javascript, json, julia, kotlin, lean, lua, magma, makefile, markdown, matlab, meson, nix, objective-c (objc), ocaml, perl, php, protobuf, python, r, ruby, rust, scala, scss, sql, svelte, swift, toml, tsx, typescript, verilog, vimscript, vue, wolfram, xml, yaml, zig.

Project config overrides global for conflicting extensions. An entry whose language name is unknown, or whose extension does not start with ., is skipped and a warning is logged to stderr (shown at the default info log level). Missing config files are ignored.

Persistence

SQLite databases stored at ~/.cache/codebase-memory-mcp/. Persists across restarts (WAL mode, ACID-safe). To reset: rm -rf ~/.cache/codebase-memory-mcp/.

Troubleshooting

Problem	Fix
`/mcp` doesn't show the server	Check `.mcp.json` path is absolute. Restart agent. Test: `echo '{}' \| /path/to/binary` should output JSON.
`index_repository` fails	Pass absolute path: `index_repository(repo_path="/absolute/path")`
`trace_path` returns 0 results	Use `search_graph(name_pattern=".PartialName.")` first to find the exact name.
Queries return wrong project results	Add `project="name"` parameter. Use `list_projects` to see names.
Binary not found after install	Add to PATH: `export PATH="$HOME/.local/bin:$PATH"`
UI not loading	Ensure you downloaded the `ui` variant and ran `--ui=true`. Check `http://localhost:9749`.

Hybrid LSP

Semantic type resolution beyond tree-sitter.

Tree-sitter alone gives a syntactic AST. That handles naming, structure, and call sites well, but it can't tell you that user.profile.display_name() resolves to Profile.display_name declared three modules away — tree-sitter doesn't track imports, generics, inheritance, or stdlib types.

codebase-memory-mcp ships a lightweight C implementation of language type-resolution algorithms, structurally inspired by and compatible with major language servers (tsserver / typescript-go, pyright, gopls, Roslyn, Eclipse JDT, rust-analyzer), embedded directly into the static binary. No language server process, no per-project setup, no API key. We call this layer Hybrid LSP: it runs alongside tree-sitter on every parse and refines CALLS, USAGE, and RESOLVED_CALLS edges with type information, so the resulting graph mirrors what an IDE "Go to Definition" would resolve.

Languages with full Hybrid LSP:

Language	What it handles
Python (new in v0.7.0)	imports + dotted submodule walks, dataclasses, `Self` return types, generics, `@property`, `match/case` class patterns, SQLAlchemy 2.0 `Mapped[T]`, Pydantic `BaseModel`, `typing.Annotated` / `ClassVar` / `Final` / `InitVar`, async/await, classmethod/staticmethod, narrowing (`isinstance` / `is not None` / walrus), `typing.cast` / `assert_type`, common stdlib (logging, pathlib, json, functools). Target ~95% resolution on idiomatic code.
TypeScript / JavaScript / JSX / TSX	generics, JSX component dispatch, JSDoc inference for plain JS, `.d.ts` declarations, module re-exports, method chaining via return-type propagation, per-file overlay chained to a shared cross-file registry
PHP (new in v0.7.0)	namespaces, traits, late-static-binding, PHPDoc inference, parameter binding, return-type inference
C# (new in v0.7.0)	global usings, file-scoped namespaces, records (incl. C# 12 primary constructors), LINQ method syntax, `async Task<T>` / `ValueTask<T>` unwrap, generic methods, `this` / `base` dispatch, `var` inference, common BCL stdlib
Go (sharpened in v0.7.0)	pre-built per-package cross-file registry, generics, embedded structs, interface satisfaction, package-aware import resolution
C / C++ (sharpened in v0.7.0)	pre-built per-language cross-file registry shared across C and C++; C side handles macros + `typedef` chains + header-vs-source linking; C++ side handles templates, namespaces, `auto` inference, and method resolution via class hierarchy
Java (new in v0.8.0)	imports (single-type, on-demand, static), class hierarchies with `this` / `super` dispatch, generics, annotations, overload matching by arity and parameter types, lambdas / method references bound to functional interfaces, field-type inference, common JDK stdlib
Kotlin (new in v0.8.0)	imports + same-package resolution, classes / objects / companion objects, extension functions, data classes, nullable-type unwrapping, scope functions (`let` / `apply` / `run` / `also` / `with`), infix calls, common stdlib
Rust (new in v0.8.0)	`use` declarations + module paths, `impl` blocks and trait methods, struct fields, generics with trait bounds, operator-trait desugaring, derive-macro method synthesis, UFCS static paths, common std prelude
Perl	packages + `@ISA` / `use parent` / `use base` inheritance with method-resolution-order dispatch, `SUPER::` calls, Exporter (`use Foo qw(...)`) import maps, `bless` / `ref($class)\|\|$class` self-type inference, qualified `Pkg::sub` static calls, curated perlfunc + CPAN OOP stdlib; unresolved receivers emit no edge (zero-edge guarantee)

Two-layer architecture:

Tree-sitter pass — fast, syntactic, runs for every one of the 158 languages. Extracts definitions, calls, imports.
Hybrid LSP pass — type-aware, runs above the tree-sitter pass per-language. Refines call edges using the import graph plus a per-file or pre-built cross-file definition registry. Languages without a Hybrid LSP pass yet fall back to textual resolution, so you always get some answer.

The result is a knowledge graph accurate enough to drive trace_path across packages, inheritance hierarchies, and stdlib calls — without paying for a language server process per project.

Language Support

158 languages, all parsed via vendored tree-sitter grammars compiled into the binary. Benchmarked against 64 real open-source repositories (78 to 49K nodes):

Tier	Score	Languages
Excellent (>= 90%)		Lua, Kotlin, C++, Perl, Objective-C, Groovy, C, Bash, Zig, Swift, CSS, YAML, TOML, HTML, SCSS, HCL, Dockerfile
Good (75-89%)		Python, TypeScript, TSX, Go, Rust, Java, R, Dart, JavaScript, Erlang, Elixir, Scala, Ruby, PHP, C#, SQL
Functional (< 75%)		OCaml, Haskell

Also supported (not yet benchmarked): Ada, Agda, Apex, Assembly (NASM), Astro, AWK, Beancount, BibTeX, Bicep, Bitbake, Blade, Cairo, Cap'n Proto, Clojure, CMake, COBOL, Common Lisp, Crystal, CSV, CUDA, D, Devicetree, Diff, .env, Elm, Emacs Lisp, F#, Fennel, Fish, FORM, Fortran, FunC, GDScript, .gitattributes, .gitignore, Gleam, GLSL, GN, Go module, Go template, GraphQL, Hare, HLSL, Hyprlang, INI, ISPC, Janet, Jinja2, JSDoc, JSON, JSON5, Jsonnet, Julia, Just, Kconfig, KDL, Lean 4, Linker Script, Liquid, LLVM IR, Luau, Magma, Makefile, Markdown, MATLAB, Mermaid, Meson, Move, Nickel, Nim, Nix, Odin, Pascal, Pkl, PO (gettext), Pony, PowerShell, Prisma, .properties, Protobuf, Puppet, PureScript, Racket, Regex, requirements.txt, ReScript, RON, reStructuredText, Scheme, Slang, Smali, Smithy, Solidity, SOQL, SOSL, Squirrel, SSH config, Starlark, Svelte, Sway, SystemVerilog, TableGen, Tcl, Teal, Templ, Thrift, TLA+, Typst, Verilog, VHDL, Vim script, Vue, WGSL, WIT, Wolfram, XML, Zsh.

Architecture

src/
  main.c              Entry point (MCP stdio server + CLI + install/update/config)
  mcp/                MCP server (15 tools, JSON-RPC 2.0, session detection, auto-index)
  cli/                Install/uninstall/update/config (43 client surfaces, hooks, instructions)
  store/              SQLite graph storage (nodes, edges, traversal, search, Louvain)
  pipeline/           Multi-pass indexing (structure → definitions → calls → HTTP links → config → tests)
  cypher/             Cypher query lexer, parser, planner, executor
  discover/           File discovery (.gitignore, .cbmignore, symlink handling)
  watcher/            Background auto-sync (git polling, adaptive intervals)
  traces/             Runtime trace ingestion
  ui/                 Embedded HTTP server + 3D graph visualization
  foundation/         Platform abstractions (threads, filesystem, logging, memory)
internal/cbm/         Vendored tree-sitter grammars (158 languages) + AST extraction engine

Security

Every release binary is verified through a multi-layer pipeline before publication:

VirusTotal — all binaries scanned by 70+ antivirus engines (zero detections required to publish)
SLSA Level 3 — cryptographic build provenance generated by the trusted GitHub Actions build workflow; verify with gh attestation verify <file> --repo DeusData/codebase-memory-mcp --signer-workflow DeusData/codebase-memory-mcp/.github/workflows/_build.yml
Sigstore cosign — keyless signatures on all artifacts; bundles included in every release
SHA-256 checksums — checksums.txt published with every release; verified by both install scripts before extraction
CodeQL SAST — blocks release pipeline if any open alerts remain
Zero runtime dependencies — no transitive supply chain; all libraries vendored at compile time

v0.7.0 VirusTotal scans

Binary	SHA-256	VirusTotal
`linux-amd64`	`8e12bb2d6ead7f20a6d3...`	0/72 ✅
`linux-arm64`	`10f7136bfbf3950c6b2a...`	0/72 ✅
`darwin-arm64`	`7062a7408906344bf4f8...`	0/72 ✅
`darwin-amd64`	`28c6d640e1a0ac7bfcab...`	0/72 ✅
`windows-amd64`	`9c3ddcf78368fd4fa891...`	0/72 ✅

Scan links for every release are also included in the GitHub Release notes automatically.

License

MIT

Name		Name	Last commit message	Last commit date
Latest commit History 1,568 Commits
.github		.github
docs		docs
graph-ui		graph-ui
internal/cbm		internal/cbm
pkg		pkg
scripts		scripts
src		src
test-infrastructure		test-infrastructure
tests		tests
tools		tools
vendored		vendored
.clang-format		.clang-format
.clang-tidy		.clang-tidy
.cppcheck		.cppcheck
.gitattributes		.gitattributes
.gitignore		.gitignore
.gitleaksignore		.gitleaksignore
CODE_OF_CONDUCT.md		CODE_OF_CONDUCT.md
CONTRIBUTING.md		CONTRIBUTING.md
DCO		DCO
Formula		Formula
LICENSE		LICENSE
MAINTAINERS.md		MAINTAINERS.md
Makefile.cbm		Makefile.cbm
README.md		README.md
SECURITY.md		SECURITY.md
THIRD_PARTY.md		THIRD_PARTY.md
flake.lock		flake.lock
flake.nix		flake.nix
glama.json		glama.json
install.ps1		install.ps1
install.sh		install.sh
server.json		server.json

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codebase-memory-mcp

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