codebase-index 1.6.0

Local-first hybrid codebase index for AI coding agents, exposed as CLI, Skill, and MCP tools.

codebase-index: Local Codebase Indexing for AI Coding Agents

codebase-index is a local-first codebase indexing tool that helps Claude Code, Codex CLI, OpenCode, and other AI coding agents find relevant files, symbols, and references without scanning an entire repository.

What Is codebase-index?

codebase-index is a private, offline retrieval layer for AI code search. It builds a SQLite index of your repository, extracts symbols with Tree-sitter, ranks matches with hybrid retrieval, and returns compact file:line ranges that an AI coding agent can read instead of opening broad file sets.

Use it when you want Cursor-like codebase awareness in terminal-based AI tools while keeping source code, snippets, and search metadata on your machine.

codebase-index is not an IDE and not a coding agent. It is the local retrieval/index layer that gives terminal and MCP-based AI agents precise codebase context. The agent stays your interface; this gives it better aim.

Who Is It For?

• Claude Code / Codex CLI / OpenCode users on medium-to-large repos who want the agent to read 3 ranked files instead of grepping and scanning 60.
• Privacy-constrained teams (proprietary or regulated code) who cannot send source to a cloud code-intelligence service.
• MCP power users who want a stable, queryable code index as a tool, not a black box baked into one agent's prompt.
• Tooling authors who need scriptable retrieval (--json, SQLite, MCP) that other tools can build on.

Not for you if you want a full IDE, org-scale multi-repo search, or a hosted platform — use Cursor or Sourcegraph for those.

Start Here

If you are opening this repository for the first time, follow this order:

1. Quick Start (5 minutes)
2. Installation Guide
3. Benchmarks
4. How the skill works
5. MCP server
6. FAQ

If you only need the shortest path, run:

pip install "codebase-index @ git+https://github.com/denfry/codebase-index.git@v1.6.0"
cd your-project
codebase-index init            # prompts for Claude Code / Codex CLI / OpenCode
codebase-index index
codebase-index search "where is authentication implemented?"

Project Status

1.6.0 is released. The current release includes repository discovery, SQLite FTS5 storage, Tree-sitter symbols and references, hybrid ranking, graph impact analysis, token-budgeted retrieval packets, optional local embeddings, hooks/watch support, multi-CLI installation, MCP server support, and a tested GitHub-only pipx install path.

The 1.6.0 release turns the dependency graph into a navigable map: every edge carries a confidence audit trail (extracted/inferred/ambiguous, surfaced in refs/impact); a new zero-dependency analytics pass computes modules (communities), god nodes, and surprising cross-module links, exposed via the architecture command/MCP tool; path traces the shortest dependency chain between two symbols and describe prints a symbol's node card; and the HTML graph is coloured by module and sized by connectivity, with --format graphml|dot|neo4j exports for external tools. Requires a one-time reindex (schema 2 → 3).

The earlier 1.4.0 release hardened the MCP contract (a schema_version + tool envelope on every payload, golden-locked per tool, plus a fix so the server loads on current mcp/pydantic), dampened the god-class in_degree rerank tiebreak (logarithmic, validated no-regression on the public benchmark), and labelled config/IaC files (Dockerfile, Terraform, HCL, INI, Makefiles) so infra surfaces in stats and search.

The earlier 1.3.0 release added a content-addressed embedding cache (rebuilds reuse vectors for unchanged content), a batched graph build (7–28× faster edge resolution plus a new edges(file_id) index), a shared CLI/MCP service layer (MCP hybrid search now uses the vector channel; index_stats reports the per-language graph tier), graph-coverage signals in stats/refs/impact, CLI pagination via search --offset, and single-source versioning with a CI gate that keeps every committed skill copy in sync. The 1.2.1 release added skill auto-update/rollback commands and version stamps so installed skills stay in sync with the package automatically. See CHANGELOG.md and docs/ROADMAP.md.

MCP is now available as a stdio server via codebase-index mcp --root <repo>. It exposes healthcheck, search_code, find_symbol, find_refs, impact_of, explain_code, architecture_overview, path_between, describe_symbol, and index_stats; see docs/MCP.md.

You:   "Where is user authentication implemented?"
Agent: searches local index (symbols + FTS5 + graph)
       reads only 3 ranked files instead of scanning 60
       answers with citations: src/auth/AuthService.ts:12-148

---

How Do I Install codebase-index?

For most users, install the package from the tagged GitHub release and run init inside the repository you want to index:

pip install "codebase-index @ git+https://github.com/denfry/codebase-index.git@v1.6.0"
cd your-project
codebase-index init            # choose Claude Code, Codex CLI, OpenCode, or all
codebase-index index

In a non-interactive script, pass a target explicitly:

codebase-index init --target auto      # install into detected AI CLIs
codebase-index init --target codex     # write AGENTS.md + Codex resources
codebase-index init --target claude    # write .claude/skills/codebase-index
codebase-index init --target opencode  # write OpenCode command + agent files

Install as a Claude Code plugin

One command in Claude Code:

/plugin marketplace add denfry/codebase-index
/plugin install codebase-index@codebase-index

Or just ask: "install the codebase-index plugin".

What happens on first run: when a session starts, a SessionStart hook (scripts/bootstrap.sh / .ps1) creates a private Python virtual environment under ~/.claude/plugins/data/codebase-index-*/venv and installs the pinned codebase-index package (from requirements.lock) into it — using uv if present, otherwise python -m venv + pip. It reinstalls only when the lock file changes. Nothing is installed globally; uninstalling the plugin removes the data directory.

Prerequisite: Python 3.11+ on your PATH. The first install needs network access to fetch the package; later sessions are offline. The skill builds its index on your first codebase question, so there is no manual index step.

Distribution note: the plugin bootstrap installs the pinned requirement from requirements.lock. In 1.6.0, that lock points at the tagged GitHub release instead of PyPI. You can override it with CBX_INSTALL_SPEC when testing a local checkout or a different Git ref.

What Problem Does codebase-index Solve?

AI coding agents struggle with large repositories when they rely on broad file reads, grep output, or user-provided context. codebase-index gives those agents a ranked local retrieval packet before they read source files.

• Token waste — Scanning entire files or running broad grep/glob queries burns through the context window on irrelevant content.
• No symbol awareness — Standard search can't distinguish a function definition from a call, or a class from a variable.
• No ranking — Grep returns all matches with no relevance ordering. The agent must read everything.
• No context — Grep doesn't know which files are related or what to read next.
• Cloud dependency — External code indexing services send your proprietary code to remote servers.

Developers get Cursor-like codebase awareness in Claude Code, Codex CLI, and OpenCode without leaving the terminal or sending code to a remote indexing service.

How Is This Different?

Short answers to the questions people actually ask. The full, honest matrix — including when you should pick the other tool — is in docs/COMPARISON.md.

• Why not just grep/rg? Grep returns every match with no ranking, no symbol awareness, and no idea which files relate. codebase-index ranks results, knows a definition from a call, expands along the dependency graph, and returns specific line ranges under a token budget — so the agent reads less and answers with citations.
• Why not Cursor? Cursor is a great AI IDE with strong codebase awareness, but it is proprietary and IDE-centric. codebase-index is a local, open retrieval layer for terminal and MCP agents, offline by default, with no IDE lock-in. If you live inside Cursor, keep using Cursor.
• Why not Aider repo-map? Aider's repo-map is a good graph-ranked, token-budgeted context map — but it is optimized to feed Aider's own chat. codebase-index is a reusable, queryable index: CLI/JSON/MCP commands return ranked file:line ranges, symbols, references, and impact that any shell-capable agent can consume, with freshness and security gates.
• Why not Sourcegraph / Cody / Amp? They are excellent enterprise-grade, cross-repo code intelligence platforms. They are also heavier and account/platform-oriented. codebase-index is single-repo, local, and lightweight — no server, no account, no code leaving the machine by default.
• Why not Codebase-Memory MCP? It is the closest direct alternative — a broader graph engine with a static binary and wide language/agent coverage. We do not claim to beat it globally. We differentiate on simplicity, a strict privacy model, token-budgeted retrieval packets, a transparent Python implementation, the Claude/Codex/OpenCode workflow, and honest benchmarks. If you need its broader graph and language reach today, choose it.

What makes it trustworthy? No telemetry, no network by default, a multi-gate exclusion pipeline (secrets/binaries/generated/dependencies never indexed), output-time secret redaction, a doctor --strict safety self-check, and a public benchmark suite wired as a CI regression gate. Claims that aren't proven in this repo are marked as roadmap, not done.

Proven today vs. roadmap

Capability	Status
Hybrid retrieval (path + symbol + FTS5 + graph), token-budgeted packets	✅ Shipped
Tree-sitter symbols for 12 Tier-A languages + Tier-B generic path	✅ Shipped
Import/call/reference/inheritance graph, refs/impact	✅ Shipped
Optional local embeddings; external embeddings gated 3 ways	✅ Shipped
stdio MCP server; CLI/skill/MCP share one service layer	✅ Shipped
Honest 55k LOC Java benchmark (recall@3 70% vs 40% rg, ~13× fewer tokens)	✅ Shipped
10k/100k/1M LOC public-repo benchmarks	🚧 Roadmap
Framework-aware typed edges (route→handler→service→model)	🚧 Roadmap
PyPI / uvx / Homebrew, signed checksums, SBOM	🚧 Roadmap
Verified per-client MCP docs, paged/progressive results	🚧 Roadmap

See docs/PRODUCT_UPGRADE_PLAN.md for the full upgrade plan and ranked roadmap.

How Does codebase-index Work?

codebase-index builds a local hybrid index that combines:

• Symbol search — Tree-sitter AST parsing extracts classes, functions, methods, and variables across the supported code-language set.
• Full-text search — SQLite FTS5 for fast lexical search across code chunks.
• Path search — File path matching for location-aware queries.
• Optional semantic search — Vector embeddings for similarity-based retrieval (opt-in, local by default).
• Dependency graph — Import, call, and reference edges for impact analysis and graph expansion.
• Token-budgeted output — Ranked retrieval packets with specific line ranges, not whole files.

The AI agent reads only the recommended files and line ranges, not the entire repository.

Quick Demo

/codebase-index "where is user authentication implemented?"

Expected output:

Top matches:
┌──────┬──────────────────────────┬──────────────────────────┬───────┬──────────────────────────────┐
│ Rank │ Path                     │ Symbols                  │ Score │ Reason                       │
├──────┼──────────────────────────┼──────────────────────────┼───────┼──────────────────────────────┤
│    1 │ src/auth/AuthService.ts  │ AuthService, login       │  0.92 │ exact symbol match           │
│    2 │ src/routes/auth.ts       │ loginHandler, logout     │  0.78 │ FTS match · 4 callers        │
│    3 │ src/middleware/auth.ts   │ requireAuth              │  0.65 │ path match · FTS match       │
└──────┴──────────────────────────┴──────────────────────────┴───────┴──────────────────────────────┘

Recommended reads:
  1. src/auth/AuthService.ts:12-148
     reason: matched AuthService, login(), validatePassword()
  2. src/routes/auth.ts:20-91
     reason: /login route calls AuthService.login()
  3. src/middleware/auth.ts:5-42
     reason: auth middleware validates sessions

Installation Options

If you are new to this repo, start with docs/QUICKSTART.md.
If you want all install options and troubleshooting, use docs/INSTALLATION.md.

Multi-CLI installer (Claude Code + Codex CLI + OpenCode): one command via install.sh / install.ps1 — see docs/installer.md.

# macOS / Linux
curl -fsSL https://raw.githubusercontent.com/denfry/codebase-index/main/install.sh | sh

# Windows PowerShell
irm https://raw.githubusercontent.com/denfry/codebase-index/main/install.ps1 | iex

Option 1: Install from a tagged GitHub release

cd your-project
pip install "codebase-index @ git+https://github.com/denfry/codebase-index.git@v1.6.0"
codebase-index init
codebase-index index

Python version compatibility

codebase-index requires Python 3.11 or newer.

If codebase-index init --target opencode fails with:

ModuleNotFoundError: No module named 'importlib.resources.abc'; 'importlib.resources' is not a package

the pipx environment was likely created with an older Python version. Reinstall codebase-index using Python 3.11+ explicitly:

pipx uninstall codebase-index
py -0p
pipx install --python "<path-to-python-3.11-or-newer>\python.exe" "git+https://github.com/denfry/codebase-index.git@v1.6.0"

For example:

pipx install --python "C:\Users\you\AppData\Local\Programs\Python\Python312\python.exe" "git+https://github.com/denfry/codebase-index.git@v1.6.0"

Then run initialization again:

codebase-index init --target opencode
codebase-index index

Option 2: Install with pipx from GitHub

pipx install "git+https://github.com/denfry/codebase-index.git@v1.6.0"
cd your-project
codebase-index init --target auto
codebase-index index

Option 3: Install from source

git clone https://github.com/denfry/codebase-index.git
cd codebase-index
pip install -e ".[dev]"

Distribution roadmap

PyPI, uvx, Homebrew, signed release checksums, and SBOMs are important for a tool that reads entire repositories, but they are not all verified as shipped in 1.6.0. Target install story:

uvx codebase-index init
pipx install codebase-index
brew install denfry/tap/codebase-index

Verify the install

codebase-index doctor

See docs/INSTALLATION.md for the full guide, including optional extras (embeddings, watch mode) and troubleshooting.

Usage

# Initialize the index for your project
codebase-index init

# Build the index
codebase-index index

# Search for something
codebase-index search "where is authentication implemented?"

# Look up a specific symbol
codebase-index symbol "AuthService"

# Find callers and references
codebase-index refs "AuthService.login"

# Analyze impact of a change
codebase-index impact "src/auth/AuthService.ts"

# Map the codebase: modules, god nodes, surprising links, suggested questions
codebase-index architecture

# How are two symbols/files connected? Shortest dependency/call path
codebase-index path "renew" "refresh_access_token"

# Node card: definition, callers, callees, centrality, module
codebase-index describe "Database"

# Visualize the graph (modules coloured, size = connectivity, edge style = confidence)
codebase-index graph --open
# …or export for external tools: graphml (Gephi/yEd), dot (Graphviz), neo4j (Cypher)
codebase-index graph --format graphml -o graph.graphml

# View index statistics
codebase-index stats

# Run diagnostics
codebase-index doctor

Add --json to any command for machine-readable output.

How Does Retrieval Flow Through codebase-index?

User question
    ↓
CLI instructions or skill
    ↓
Hybrid retrieval
    ├─ Path search
    ├─ Symbol search (Tree-sitter AST)
    ├─ SQLite FTS5 full-text search
    ├─ Optional embeddings (vector search)
    └─ Graph expansion (callers, imports, references)
    ↓
Ranked retrieval packet
    ↓
Agent reads only the recommended line ranges
    ↓
Answer with precise file:line citations

Features

• Local-first indexing — All data stays on your machine
• No network by default — Zero external API calls out of the box
• Respects ignore files — .gitignore, .claudeignore, .codeindexignore
• SQLite storage — Fast, reliable, single-file database
• FTS5 lexical search — Full-text search with code-aware tokenization
• Tree-sitter AST parsing — Tier-A symbol extraction for Python, JavaScript, TypeScript, Java, Go, Rust, C, C++, C#, Ruby, PHP, and Kotlin; Tier-B generic extraction for code languages with a loadable grammar such as Lua
• Symbol extraction — Classes, functions, methods, variables with line ranges
• Incremental indexing — Only changed files are re-indexed
• Token-budgeted output — Configurable max output size
• Secret redaction — Masks keys, tokens, and credentials in snippets
• Optional embeddings — Local or remote vector search (opt-in)
• Optional hooks/watch — Auto-update index after file edits
• Multi-CLI setup — Claude Code, Codex CLI, and OpenCode instructions
• MCP server — stdio MCP tools for search, symbols, refs, impact, explain, health, and stats

Safety and Privacy

Trust model in 60 seconds

1. Offline by default — the base install has zero network dependencies; nothing leaves your machine.
2. One opt-in exit, triple-gated — external embeddings require allow_external and an env API key and a printed endpoint warning, or they are refused.
3. Secrets never get in — .env, keys, certs, and credential files are excluded before parsing (multi-gate ignore pipeline).
4. Secrets never get out — every snippet is redacted (AWS keys, private keys, JWTs, bearer tokens, connection strings) before it reaches the agent.
5. No telemetry, ever — no analytics, no phone-home, no usage data.
6. Verify it yourself — codebase-index doctor --strict audits all of the above and exits non-zero in CI on any high-severity finding.

codebase-index is designed with privacy as a first principle:

• No telemetry — No usage data, analytics, or crash reports are collected or transmitted.
• No external API calls by default — All indexing, storage, and search happen locally.
• Does not index sensitive files — .env, private keys, certificates, tokens, and credential files are excluded before parsing.
• Respects ignore files — .gitignore, .claudeignore, .codeindexignore, and .cursorignore are all honored.
• Index stored locally — SQLite database in .claude/cache/codebase-index/ (gitignored by default).
• Optional embeddings are local by default — External embedding APIs require explicit opt-in with warnings.
• Secret redaction — Snippets are scrubbed for AWS keys, private keys, JWTs, bearer tokens, and connection strings before output.

See docs/SECURITY_MODEL.md for the full security model and threat analysis.

Benchmark Results

There are three benchmark surfaces today:

1. Public benchmark suite in tests/benchmark_public.py: reproducible multi-language fixture with Recall@1/3/5, MRR, nDCG, answer-correctness proxy, token economy, language breakdown, freshness latency, graph tasks, and scale counters.
2. Smoke benchmark on sample_repo: validates the CLI is fast and stable on a tiny fixture, but it is not evidence of production retrieval quality.
3. Honest benchmark on a real Java repository: tests/benchmark_honest.py compares codebase-index against a disciplined rg + read-window baseline on 10 realistic questions. Results are documented in tests/benchmark_honest_RESULTS.md.

Run the public suite:

python tests/benchmark_public.py --workdir .tmp-public-benchmark

Current honest benchmark headline:

Metric	Result
Repo	303 Java files, ~55k LOC
Retrieval quality	recall@3: 70% index vs 40% rg baseline
Token economy	~13x fewer answer tokens than rg + 80-line windows
Verified language impact	Java symbols fixed from 0 to 3,543 symbols

The public suite now has the metric framework. It still needs larger public or documented external repos for 10k/100k/1M LOC scale claims and deeper framework graph tasks. See docs/BENCHMARKS.md.

Repository Layout

├── skill/              # Source instruction package (SKILL.md, scripts, examples)
├── skills/             # Plugin skill copy
├── src/codebase_index/ # Python package (CLI, indexer, retrieval, storage)
├── docs/               # Documentation (architecture, schema, security, FAQ)
├── examples/           # Sample queries, retrieval output, demo project
├── tests/              # Test suite with fixture repositories
├── bin/                # Plugin CLI wrappers (cbx, codebase-index)
├── scripts/            # Bootstrap scripts (bootstrap.sh, bootstrap.ps1)
├── hooks/              # Plugin hooks (hooks.json)
├── .claude-plugin/     # Plugin manifest + marketplace catalog
├── .github/            # Issue templates, CI workflows, PR template
├── README.md           # This file
├── LICENSE             # MIT License
├── CHANGELOG.md        # Release history
├── CONTRIBUTING.md     # Contributor guide
├── SECURITY.md         # Security policy
├── ROADMAP.md          # Development milestones
├── requirements.lock   # Pinned install spec for bootstrap
└── pyproject.toml      # Package configuration

Configuration

Create .codeindex.json in your project root:

{
  "index": {
    "max_file_bytes": 1048576,
    "chunk_size": 500,
    "chunk_overlap": 50
  },
  "embeddings": {
    "backend": "noop",
    "allow_external": false
  }
}

Ignore Files

• .codeindexignore — Tool-specific ignore patterns (highest priority)
• .gitignore — Standard git ignore patterns
• .claudeignore — Claude-specific ignore patterns

Cache Location

.claude/cache/codebase-index/
├── index.sqlite   # SQLite database with FTS5
└── config.json    # Resolved configuration

Which AI CLIs Does codebase-index Support?

codebase-index init can install instructions for three AI coding CLIs:

CLI	Files written by init	Best command
Claude Code	.claude/skills/codebase-index/	codebase-index init --target claude
Codex CLI	AGENTS.md + .codex/skills/codebase-index/	codebase-index init --target codex
OpenCode	.opencode/commands/ + .opencode/agents/ + resources	codebase-index init --target opencode

Use codebase-index init --target auto to install into detected CLIs, or codebase-index init --target all to write every supported integration.

Claude Code Integration

The Claude Code skill is defined in skill/SKILL.md with YAML frontmatter for automatic selection.

Example .claude/CLAUDE.md:

## Codebase Questions

Before answering any question about this project's code:
1. Use the codebase-index skill to search the local index first.
2. Read only the recommended line ranges — do not scan entire files.
3. Answer with file:line citations.

Optional Hooks

Configure automatic index updates in .codeindex.json:

{
  "hooks": {
    "post_tool_use": {
      "enabled": true,
      "events": ["Write", "Edit"],
      "command": "codebase-index update --quiet"
    }
  }
}

See skill/examples/ for full examples.

FAQ

Is this a Cursor replacement?

No. codebase-index is not a replacement for Cursor or any IDE. It is a local retrieval layer for terminal AI coding agents. You still use Claude Code, Codex CLI, OpenCode, or another agent as your primary interface.

Does it send my code anywhere?

No. By default, codebase-index is completely local-first and offline. All indexing, storage, and search happen on your machine. External embeddings are opt-in only and require explicit configuration.

Does it work without embeddings?

Yes. The default configuration disables embeddings entirely (backend = "noop"). Search uses SQLite FTS5, Tree-sitter symbol extraction, path matching, and graph expansion. Embeddings are an optional enhancement.

Does it support large repositories?

Yes. The index is incremental — only changed files are re-indexed. SQLite with FTS5 handles large datasets efficiently. Generated files, dependencies, and binaries are excluded automatically.

Why not just use Grep?

Grep returns all matches with no ranking, no symbol awareness, and no context about related files. codebase-index combines lexical search with symbol extraction and graph expansion to return ranked, contextual results with specific line ranges to read.

Does it support MCP?

Yes. Run codebase-index mcp --root <repo> to expose the local index over stdio MCP. See docs/MCP.md for tools and client config templates.

Can I use it with other agents?

Yes. The CLI is agent-agnostic. Any agent that can run shell commands can use codebase-index, and JSON output (--json) is parseable by other tools.

How do I reset the index?

codebase-index clean          # reset the index DB (keeps the skill)
codebase-index clean --all    # wipe the whole .claude/cache/codebase-index/ dir
# Or manually: rm -rf .claude/cache/codebase-index/
codebase-index index

Contributing

We welcome contributions! See CONTRIBUTING.md for the full guide.

Quick start:

git clone https://github.com/denfry/codebase-index.git
cd codebase-index
pip install -e ".[dev]"
pytest
ruff check src/ tests/

Roadmap

See ROADMAP.md for the full milestone plan.

Milestone	Status	Description
M0	✅ Done	Repository packaging
M1	✅ Done	SQLite + FTS5 index
M2	✅ Done	Tree-sitter symbol extraction
M3	✅ Done	Hybrid retrieval
M4	✅ Done	Graph expansion
M5	✅ Done	Token-budgeted retrieval packets
M6	✅ Done	Optional local embeddings
M7	✅ Done	Claude Code Skill packaging
M7.5	✅ Done	One-command plugin install
M8	✅ Done	Hooks + watch mode
M9	✅ Done	Public release

License

MIT