Code Indexing MCP

Code Indexing MCP is a local-only codebase indexer for MCP clients. It uses Tree-sitter to extract syntax-aware chunks, FastEmbed to create embeddings on the local machine, and LanceDB for persistent vector and full-text search.

It does not require a hosted database, embedding API, daemon, or network transport. The only network access is the initial download of the default jinaai/jina-embeddings-v2-base-code model (approximately 640 MB). Once cached, indexing and search work offline.

Install

• Git

• uv

• Python 3.12 or 3.13

On macOS or Linux:

curl -fsSL https://raw.githubusercontent.com/MarcinHamiga/code-indexing-mcp/main/install.sh | sh

On Windows PowerShell:

$installer = Join-Path $env:TEMP "code-indexing-mcp-install.py"
Invoke-WebRequest https://raw.githubusercontent.com/MarcinHamiga/code-indexing-mcp/main/install.py -OutFile $installer
py -3 $installer

The installer clones the repository to ~/.local/share/code-indexing-mcp, creates its locked virtual environment, and displays this multi-select menu:

1. Codex (CLI + Desktop)

2. Claude Code

3. Kimi Code

4. Claude Desktop

5. OpenCode

6. KiloCode

Codex CLI and Codex Desktop share one configuration and therefore use one menu choice. Configuration changes are limited to the code-indexing-mcp entry. An existing configuration is backed up alongside the original with a .bak suffix before it changes.

Run the same command later to update an existing clean checkout with a fast-forward-only pull and refresh its environment. The installer refuses to overwrite a different repository or a checkout with local changes.

For a noninteractive installation, pass comma-separated harness slugs or all:

curl -fsSL https://raw.githubusercontent.com/MarcinHamiga/code-indexing-mcp/main/install.sh |
  sh -s -- --harnesses codex,claude-code,opencode

Use --install-dir /custom/path or CODE_INDEXING_MCP_INSTALL_DIR to change the checkout location. Run python3 install.py --help for all installer options.

Related MCP server: agentmako

Manual setup

git clone https://github.com/MarcinHamiga/code-indexing-mcp.git
cd code-indexing-mcp
uv sync --locked
uv run code-indexing-mcp model pull

The model preparation step is optional; the first index operation downloads the model when it is not already cached.

MCP configuration

Run the server over stdio:

uv run code-indexing-mcp serve

A generic MCP client configuration looks like this:

{
  "mcpServers": {
    "code-indexing-mcp": {
      "command": "uv",
      "args": [
        "--directory",
        "/absolute/path/to/code-indexing-mcp",
        "run",
        "code-indexing-mcp",
        "serve"
      ]
    }
  }
}

The server exposes init_project, index_project, project_status, list_projects, remove_project, search_code, find_symbol, file_outline, and get_chunk.

Project workflow

cd /path/to/project
uv run --project /path/to/code-indexing-mcp code-indexing-mcp init
uv run --project /path/to/code-indexing-mcp code-indexing-mcp index
uv run --project /path/to/code-indexing-mcp code-indexing-mcp status

Initialization creates .ci-mcp/project.toml and a self-ignoring .ci-mcp/.gitignore. The marker contains a checkout-local UUID and scanning configuration. It is not intended to be committed. Markers created by earlier releases under .incode remain readable, but all new markers use .ci-mcp.

CLI index refreshes are explicit and incremental. When the MCP server is opened by a client that provides filesystem roots, it also starts an incremental background refresh for each qualifying root as soon as the client lists tools. A new root qualifies when it has at least one supported, non-ignored source file and contains .git, pyproject.toml, setup.py, setup.cfg, package.json, tsconfig.json, or jsconfig.json. The server creates the usual local .ci-mcp/project.toml marker only after that check passes.

Tool discovery returns without waiting for indexing or the first model download. project_status reports startup state, while code-query tools wait for that root's initial indexing task to finish. Set INCODE_AUTO_INDEX=0 (or false or no) to retain fully manual MCP indexing. Clients that do not provide filesystem roots keep the existing manual workflow.

Incremental refreshes:

• Matching size and nanosecond mtime skips reading the file.

• Changed metadata triggers SHA-256 verification.

• Unchanged content is neither parsed nor embedded.

• Changed files are replaced transactionally in LanceDB.

• Removed files are deleted from the active index.

• A parse or embedding failure preserves the previous indexed version.

Python, Python stubs, Java, JavaScript, JSX, TypeScript, and TSX are supported. Java indexing extracts classes, interfaces, records, enums, annotation types, methods, constructors, and nested declarations without requiring a JDK, Maven, or Gradle. The scanner respects root and nested .gitignore files and excludes symlinks, binary files, files over 1 MiB, build outputs, virtual environments, and dependency directories.

Existing project markers that use the exact pre-Java default include list automatically include **/*.java at runtime. If you use a customized scan.include list, add **/*.java explicitly.

Multi-project search

Tools use the current MCP root or nearest .ci-mcp/project.toml by default. search_code can instead receive a list of project IDs/names/paths or set all_projects=true. Searching all projects is always explicit, preventing accidental context mixing.

remove_project deletes only central index data. It never removes source files or the local .ci-mcp marker.

Storage and offline operation

Platform-specific user data and cache locations are selected with platformdirs. Override them when needed:

export INCODE_DATA_DIR=/path/to/index-data
export INCODE_CACHE_DIR=/path/to/model-cache
export INCODE_OFFLINE=1

With INCODE_OFFLINE=1, Code Indexing MCP will not download a missing model and returns MODEL_UNAVAILABLE instead. Source code, embeddings, and search queries remain local; there is no telemetry.

Development

uv run pytest
uv run pytest --cov=incode_mcp
uv run ruff check .
uv run ruff format --check .
uv run mypy src

To exercise the real model integration, provide a persistent cache directory and opt in:

INCODE_MODEL_TEST_CACHE=/path/to/cache uv run pytest -m model

V1 intentionally excludes filesystem watching, HTTP transports, dependency/call graphs, cross-reference resolution, custom embedding profiles, and automatic storage migrations.

License

This project is licensed under the MIT License.