codeintel

# codeintel

<!-- mcp-name: io.github.phuongddx/codeintel -->

**Local-first code intelligence for coding agents.** Precomputed SCIP navigation
(go-to-definition, find-references, call hierarchy, document symbols), Zoekt
lexical search, cross-repo blast radius, and semantic search — exposed as MCP
tools to Claude Code, Cursor, or any MCP client.

Runs as a single stdio process reading local SQLite files. **No server, no auth,
no network, nothing leaves your machine.**

## Quick Start

```bash
# 1. External indexer binaries (scip, zoekt, per-language indexers)
curl -fsSL https://raw.githubusercontent.com/phuongddx/codeintel/main/setup.sh | sh

# 2. codeintel itself
uv tool install codeintel-navigation-mcp

# 3. Index a repo (slug defaults to the directory name)
codeintel index /path/to/your/repo
```

**4. Register the MCP server.** Using Claude Code, install the plugin and it
registers itself:

```
/plugin marketplace add phuongddx/codeintel
/plugin install codeintel@codeintel
```

Any other MCP client (or Claude Code without the plugin) registers manually:

```bash
claude mcp add codeintel --scope user -- codeintel-server
```

That's it — ask your agent "find all references to `AuthService`" and it will
call `findReferences` instead of grepping.

<details>
<summary>Other MCP clients (Cursor, Claude Desktop, any stdio client)</summary>

```json
{
  "mcpServers": {
    "codeintel": {
      "command": "codeintel-server"
    }
  }
}
```

If your client can't find `codeintel-server` on `PATH` (GUI apps often don't
inherit your shell's), use the absolute path from `which codeintel-server`.
</details>

<details>
<summary>Running from a clone instead</summary>

```bash
git clone https://github.com/phuongddx/codeintel && cd codeintel
uv sync
claude mcp add codeintel --scope user -- uv --directory "$(pwd)" run codeintel-server
```
</details>

## MCP tools

| Tool | What it does |
|------|--------------|
| `goToDefinition` | Resolve a symbol to its defining file and range |
| `findReferences` | Every occurrence of a symbol across the indexed repo |
| `callHierarchy` | Incoming/outgoing calls for a symbol |
| `documentSymbols` | Outline of every symbol defined in one file |
| `searchCode` | Zoekt lexical/regex search, optionally filtered to one repo |
| `semanticSearch` | Natural-language search — vector hits fused with Zoekt via reciprocal rank fusion |
| `blastRadius` | Which *other* indexed repos depend on a package, up to 2 hops |
| `getIndexStatus` | Published commit, freshness, staleness vs. a working tree |
| `typeHierarchy` | Supertypes/subtypes — **currently non-functional**, see [limitations](#known-upstream-limitations) |

Every nav tool takes `repo` (the slug from `codeintel index`) plus a
tool-specific `symbol` or `path`. All tools report failure the same way — a
`{"error": "..."}` payload rather than a transport-level error, so a query bug
never kills the stdio server.

## Requirements and limits

Read this before installing — codeintel is deliberately narrow.

- **macOS and Linux only.** Windows is not supported.
- **One language per repo.** Language is detected by extension plurality across
  git-tracked files; a polyglot monorepo gets indexed as whichever language has
  the most files. Multi-language merge is out of scope. Override with
  `--language`.
- **SCIP navigation (`goToDefinition`, `findReferences`, etc.) covers four
  language families:** TypeScript/TSX, Python, Java/Kotlin, Swift.
  `codeintel index --search-only` additionally covers Go, Ruby, Rust, C,
  C++, C#, PHP, Scala, shell, and SQL for `searchCode`/`semanticSearch`
  only — no navigation.
- **Navigation and search only — codeintel never edits code.** If you want an
  agent that can perform semantic renames and refactors, you want
  [Serena](https://github.com/oraios/serena); the two are complementary.
- **Indexing is a separate, explicit step.** Nothing is live-analyzed. Run
  `codeintel index` (or `codeintel watch`) to publish an index before querying.
- **Requires external binaries** that `setup.sh` installs:

  | Purpose | Binary | Source |
  |---------|--------|--------|
  | SCIP → SQLite conversion | `scip` | prebuilt, pinned `v0.9.0` (**minimum** — older versions silently drop occurrence ranges) |
  | Lexical search | `zoekt-index` · `zoekt-webserver` | cross-compiled by [our CI](.github/workflows/build-zoekt.yml) — upstream publishes no binaries |
  | TypeScript indexing | `scip-typescript` | `npm install -g` |
  | Python indexing | `scip-python` | `npm install -g` |
  | Swift indexing | `scip-swift` | prebuilt, **macOS arm64 only** |
  | Java/Kotlin indexing | `scip-java` | detect-only — Docker image, asks before pulling |

  Options: `--only <name>` to install one dependency, `--force` to reinstall,
  `--help` for usage. Re-running is safe: anything already present is skipped.

Optional extras:

```bash
uv tool install "codeintel-navigation-mcp[watch]"      # + watchdog, for `codeintel watch`
uv tool install "codeintel-navigation-mcp[semantic]"   # + lancedb/sentence-transformers/tree-sitter, for semanticSearch
```

## Why it's built this way

**Overview** — client, server, the 3 engines (Query / Search / Graph), and storage:

![codeintel overview](docs/assets/codeintel-architecture.png)

**Index pipeline & package graph** — how `codeintel index` builds and publishes
an index, how the package dependency graph feeds `blastRadius`, and how
`codeintel watch` debounces a burst of edits into one reindex:

![codeintel index pipeline and package graph](docs/assets/codeintel-system-architecture.png)

Three things worth reading the diagrams for:

- **The runtime path never writes.** Queries open a published `index-<sha>.db`
  read-only (`mode=ro&immutable=1`). Index files are never mutated in place.
- **Publishing is atomic.** A reindex writes a new versioned `.db`, populates
  the package graph, and runs `zoekt-index` — only once *all* of that succeeds
  does `os.replace` (POSIX `rename(2)`) flip the small `current` pointer. A
  query already reading the old file keeps working; there is no downtime
  window, and a failure anywhere leaves the previously published index live.
- **The package graph is rebuilt, not accumulated.** Each reindex clears that
  repo's own outgoing edges before recomputing them, so a removed dependency's
  edge is retracted — `blastRadius` always reflects each repo's *last* index
  run.

Editable sources:
[`docs/assets/codeintel-architecture.excalidraw`](docs/assets/codeintel-architecture.excalidraw) ·
[`docs/assets/codeintel-system-architecture.excalidraw`](docs/assets/codeintel-system-architecture.excalidraw)

Core query/search logic is ported from an internal reference implementation;
the enterprise shell (FastAPI, Postgres, hosted-git auth, Cloud Build) is
dropped in favor of a single stdio process reading local SQLite files.

## Indexing a repo

```bash
codeintel index /path/to/your/repo            # slug defaults to the directory name
codeintel index /path/to/your/repo --slug foo # or pick one explicitly
codeintel index /path/to/your/repo --scheme MyScheme # Swift repo with an ambiguous Xcode scheme
codeintel index /path/to/your/repo --language python # force the language instead of detecting it from git-tracked files
codeintel index /path/to/your/repo --semantic-include vendor/generated # force-include a path the generated-file filter would otherwise skip
codeintel index /path/to/your/repo --search-only # skip SCIP indexing; publish only Zoekt + semantic search
codeintel list
codeintel status foo
codeintel reindex foo
codeintel forget foo
```

`status` (as shown by both `list` and `status`) is usually `indexed` or
`failed`, but can also be `partial`: the index published real symbols but no
navigable positions (an indexer/converter bug) — check the stderr warning
from `codeintel index` for details.

`--semantic-include` is repeatable — pass it once per path prefix to
force-include several. Like `--scheme` and `--language`, once set there is no flag to clear
it; change it by re-running `codeintel index` with the new value(s).

**Language detection** counts source files by extension **across git-tracked files** and picks the winner —
one language per index:

| Extensions | Indexer |
|------------|---------|
| `.ts` `.tsx` | `scip-typescript` |
| `.py` | `scip-python` |
| `.java` `.kt` | `scip-java` |
| `.swift` | `scip-swift` |

Ties break by fixed priority (`.ts` → `.tsx` → `.py` → `.java` → `.kt` → `.swift`).
`.git`, `node_modules`, `.venv`, `__pycache__`, `dist`, and `build` are
skipped. Reading git rather than walking the filesystem is deliberate: a walk
also counts gitignored scratch directories, which can outnumber a repo's own
code and pick a language it doesn't use.

The pipeline then runs: chosen indexer → `scip expt-convert` → populate the
package dependency graph (`packages`/`edges` tables in `registry.db`) →
`zoekt-index` into `~/.codeintel/.zoekt` → copy to
`~/.codeintel/scip/_/<slug>/_/index-<sha>.db` → atomic `current` pointer flip →
registry update.

> The `scip/_/<slug>/_/` path shape reuses the vendored `IndexConnectionCache`'s
> `(project, repo, branch)` 3-tuple layout with the outer two pinned to `_` (see
> [`src/codeintel/config.py`](src/codeintel/config.py)). It is not a user-facing
> contract — only `<slug>` matters when calling tools.

Swift indexing works end-to-end. It requires `scip >= v0.9.0`: older converters
cannot read scip.proto's `typed_range` oneof, which is the only range encoding
`scip-swift` emits, and silently produce an index with no navigable positions.
`codeintel index` refuses an older `scip` rather than publishing one.

Indexing a Swift repo with code-signed app-extension targets additionally requires
`scip-swift >= v0.1.2`: earlier versions pass no code-signing overrides to `xcodebuild`, which
then fails provisioning for every signed target before compiling anything. Because `setup.sh`
skips any dependency that is merely *present*, an existing install is **not** u