aptu-coder 0.29.1

<p align="center">

<h1 align="center">aptu-coder</h1>

<p align="center">
  <a href="https://crates.io/crates/aptu-coder"><img alt="crates.io" src="https://img.shields.io/crates/v/aptu-coder.svg?style=for-the-badge&color=fc8d62&logo=rust" height="20"></a>
  <a href="https://slsa.dev"><img alt="SLSA Level 3" src="https://img.shields.io/badge/SLSA-Level%203-green?style=for-the-badge" height="20"></a>
  <a href="https://www.bestpractices.dev/projects/12275"><img alt="OpenSSF Best Practices" src="https://img.shields.io/cii/level/12275?style=for-the-badge" height="20"></a>
</p>

<p align="center">Standalone MCP server for code structure analysis using tree-sitter. OpenSSF silver certified: fewer than 1% of open source projects reach this level.</p>

<!-- mcp-name: io.github.clouatre-labs/aptu-coder -->

> [!NOTE]
> Native agent tools (regex search, path matching, file reading) handle targeted lookups well. `aptu-coder` handles the mechanical, non-AI work: mapping directory structure, extracting symbols, and tracing call graphs. Offloading this to a dedicated tool reduces token usage and speeds up coding with better accuracy.

## Benchmarks

Auth migration task on Claude Code against [Django](https://github.com/django/django) (Python) source tree. [Full methodology](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/benchmarks/v12/methodology.md).

| Mode | Sonnet 4.6 | Haiku 4.5 |
|---|---|---|
| MCP | 112k tokens, $0.39 | 406k tokens, $0.42 |
| Native | 276k tokens, $0.95 | 473k tokens, $0.53 |
| **Savings** | **59% fewer tokens, 59% cheaper** | **14% fewer tokens, 21% cheaper** |

AeroDyn integration audit task on Claude Code against [OpenFAST](https://github.com/OpenFAST/openfast) (Fortran) source tree. [Full methodology](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/benchmarks/v13/methodology.md).

| Mode | Sonnet 4.6 | Haiku 4.5 |
|---|---|---|
| MCP | 472k tokens, $1.65 | 687k tokens, $0.72 |
| Native | 877k tokens, $2.85 | 2162k tokens, $2.21 |
| **Savings** | **46% fewer tokens, 42% cheaper** | **68% fewer tokens, 68% cheaper** |

## Overview

aptu-coder is a Model Context Protocol server that gives AI agents precise structural context about a codebase: directory trees, symbol definitions, and call graphs, without reading raw files. It supports 18 languages (see [Supported Languages](#supported-languages)) and integrates with any MCP-compatible orchestrator.

## Supported Languages

| Language | Extensions |
|----------|------------|
| Astro | `.astro` |
| C/C++ | `.c`, `.cc`, `.cpp`, `.cxx`, `.h`, `.hpp`, `.hxx` |
| C# | `.cs` |
| CSS | `.css` |
| Fortran | `.f`, `.f77`, `.f90`, `.f95`, `.f03`, `.f08`, `.for`, `.ftn` |
| Go | `.go` |
| HTML | `.html`, `.htm` |
| Java | `.java` |
| JavaScript | `.js`, `.mjs`, `.cjs` |
| JSON | `.json` |
| Kotlin | `.kt`, `.kts` |
| Markdown | `.md`, `.mdx` |
| Python | `.py` |
| Rust | `.rs` |
| TOML | `.toml` |
| TSX | `.tsx` |
| TypeScript | `.ts` |
| YAML | `.yaml`, `.yml` |

## Installation

### Homebrew (macOS and Linux)

```bash
brew install clouatre-labs/tap/aptu-coder
```

Update: `brew upgrade aptu-coder`

### cargo-binstall (no Rust required)

```bash
cargo binstall aptu-coder
```

### cargo install (requires Rust toolchain)

```bash
cargo install aptu-coder
```

## Quick Start

### Build from source

```bash
cargo build --release
```

The binary is at `target/release/aptu-coder`.

### Configure MCP Client

Two transports are available. **Streamable HTTP is recommended** when using orchestrators that spawn delegates (e.g. goose coder): a single server process is shared across the orchestrator and all agents, eliminating extension-drift that occurs when each stdio subprocess gets its own isolated instance.

**Streamable HTTP (recommended for multi-agent setups)**

With Homebrew, one command starts the server on login and keeps it running:

```bash
brew services start aptu-coder
```

The Homebrew formula starts the server on port `49200` by default. Then add the extension once to `~/.config/goose/config.yaml`:

```yaml
extensions:
  aptu-coder:
    type: streamable_http
    uri: http://127.0.0.1:49200/mcp
    name: aptu-coder
    timeout: 300
```

Or for Claude Code:

```bash
claude mcp add --transport http aptu-coder http://127.0.0.1:49200/mcp
```

To use a different port, set `APTU_CODER_PORT` before restarting:

```bash
APTU_CODER_PORT=4000 brew services restart aptu-coder
```

To start directly without brew services:

```bash
aptu-coder --port 49200
# or equivalently
APTU_CODER_PORT=49200 aptu-coder
```

**stdio (single-client use)**

Suitable when only one process needs the server. The client owns the process lifecycle and spawns it automatically:

```bash
claude mcp add --transport stdio aptu-coder -- aptu-coder
```

Or add manually to `.mcp.json` at your project root (shared with your team via version control):

```json
{
  "mcpServers": {
    "aptu-coder": {
      "command": "aptu-coder",
      "args": []
    }
  }
}
```

## Tools

All optional parameters may be omitted. Shared optional parameters for `analyze_directory`, `analyze_file`, and `analyze_symbol`:

| Parameter | Type | Default | Description |
|-----------|------|---------|-------------|
| `summary` | boolean | auto | Compact output; auto-triggers above 50K chars |
| `cursor` | string | -- | Pagination cursor from a previous response's `next_cursor` |
| `page_size` | integer | 100 | Items per page |

| Tool | Purpose | Languages |
|------|---------|-----------|
| `analyze_directory` | Directory tree with LOC, function, and class counts; respects `.gitignore` | all |
| `analyze_file` | Functions, classes, and imports with signatures and line ranges; returns graceful fallback (line count, file head, no AST) for unsupported extensions | all |
| `analyze_module` | Lightweight function and import index (~75% smaller than `analyze_file`); returns graceful fallback (empty index with note) for unsupported extensions | all |
| `analyze_symbol` | Call graph for a named symbol across a directory; callers, callees, call depth | all |
| `edit_overwrite` | Create or overwrite a file; creates parent directories | any file |
| `edit_replace` | Replace a unique exact text block or all non-overlapping occurrences (replace_all=true); errors if zero or multiple matches; empty `new_text` deletes the block; CRLF normalized before matching; optional expected_content_hash (blake3 hex of raw bytes) rejects stale edits; concurrent edits to the same file are serialized per-path; returns occurrences_replaced count | all |
| `exec_command` | Run a shell command; returns stdout, stderr, exit code; output capped and filtered; optional `timeout_secs` (kill on expiry) and `drain_timeout_secs` (post-exit drain window); heredoc rejected before spawn (file-write pattern, stdin-consuming flag, stdin parameter conflict, or missing closing delimiter) | any |

Tool parameters, constraints, and examples are available via your MCP client's tool inspector or `tools/list` response.

## MCP Resources

The knowledge graph feature exposes three MCP resource templates for navigating the structural graph built during `analyze_symbol` calls. Resources are URI-addressed; use `resources/templates/list` to discover available templates.

| URI Template | Description |
|---|---|
| `aptu-coder://graph/{repo_hash}/blast-radius/{symbol}?depth={depth}` | BFS traversal from a symbol outward to configurable depth (default: 3). Returns caller/callee chains in a radial layout. |
| `aptu-coder://graph/{repo_hash}/import-closure/{module}` | All files that directly or transitively import the given module path. |
| `aptu-coder://graph/{repo_hash}/subgraph/{symbol}` | The full subgraph (callers, callees, and their connections) for a single symbol. |

**Pagination:** Results are paginated; pass the opaque `cursor` value from a previous response to fetch the next page.

**Depth parameter:** The `blast-radius` template accepts an optional `depth` query parameter (integer, default 3).

**Cold cache:** Call `analyze_symbol` on the directory first to build the graph. Resources return an informational message until the graph is available.

## Output Management

For large codebases, several mechanisms prevent context overflow.

**Pagination**

`analyze_file` and `analyze_symbol` append a `NEXT_CURSOR:` line when output is truncated. Pass the token back as `cursor` to fetch the next page. `summary=true` and `cursor` are mutually exclusive; passing both returns an error.

```
# Response ends with:
NEXT_CURSOR: eyJvZmZzZXQiOjUwfQ==

# Fetch next page:
analyze_symbol path: /my/project symbol: my_function cursor: eyJvZmZzZXQiOjUwfQ==
```

**exec_command output caps**

`exec_command` applies three independent byte-level caps to prevent large command outputs from flooding the context:

| Stream | Cap | Behavior |
|--------|-----|----------|
| stdout | 30,000 chars | Tail-preserving; keeps the last 30k chars |
| stderr | 10,000 chars | Tail-preserving; errors appear at the end |
| combined `output_text` | 50,000 chars | Safety net after interleaving |

The 30k stdout cap is data-driven: analysis of 27,981 observed `exec_command` calls shows only 0.33% exceed this limit. When any cap fires, `output_truncated: true` is set in the response and recorded in the JSONL metrics.

`drain_timeout_secs` controls how long the server waits after the child exits for any background subprocess still holding the pipe open. Default is 500 ms (0 or omitted). Negative values return INVALID_PARAMS. When the drain window expires before the pipe closes, `output_truncated: true` is set.

**exec_command output filters**

A built-in filter table suppresses per-file noise from chatty CLI tools before output reaches the model. Filters apply to stdout, stderr, and interleaved output on success only; raw output is always preserved on failure.

| Command | Behavior |
|---------|----------|
| `git pull` | Strips diff-stat noise (pipe bars, `create mode`, `delete mode`, `rename`, `mode change` lines); empty output replaced with `ok (up-to-date)` |
| `git fetch` | Strips `From` and ref-range lines; caps at 10 lines; empty output replaced with `ok fetched` |
| `git push` | Strips `remote:` progress lines and `To ` destination lines; caps at 10 lines; empty output replaced with `ok pushed` |
| `git log` | Caps at 20 lines |
| `git status` | Caps at 20 lines |
| `git show` | Strips patch hunks (`@@` headers and `+`/`-` diff lines); caps at 200 lines |
| `git commit` | Strips GPG signing and gitleaks hook output; caps at 10 lines; empty output replaced with `ok committed` |
| `git diff` | Strips ANSI escape sequences; caps at 100 lines; empty output replaced with `ok (working tree clean)` |
| `git add` | Strips gitleaks hook output; caps at 5 lines; empty output replaced with `ok staged` |
| `cargo build` | Strips `Compiling` / `Checking` / `Downloading` / `Fresh` lines; empty output replaced with `ok (build clean)` |
| `cargo test` | Strips `Compiling` / `Checking` / `Fresh` lines |

Project-local rules can be added in `.aptu/filters.toml`. Parse errors and unrecognized schema_version values (version != 1) fall back to the built-in table with a logged warning; no crash occurs. When a filter fires, `filter_applied` in `structuredContent` identifies which rule matched.

## Non-Interactive Pipelines

In single-pass subagent sessions, prompt caches are written but never reused. Benchmarks showed MCP responses writing ~2x more to cache than native-only workflows, adding cost with no quality gain. Set `DISABLE_PROMPT_CACHING=1` (or `DISABLE_PROMPT_CACHING_HAIKU=1` for Haiku-specific pipelines) to avoid this overhead.

The server's own instructions expose a 4-step recommended workflow for unknown repositories: survey the repo root with `analyze_directory` at `max_depth=2`, drill into the source package, run `analyze_module` on key files for a function/import index (or `analyze_file` when signatures and types are needed), then use `analyze_symbol` to trace call graphs. MCP clients that surface server instructions will present this workflow automatically to the agent.

## Environment Variables

### Cache and runtime

| Variable | Default | Description |
|---|---|---|
| `APTU_CODER_DIR_CACHE_CAPACITY` | `20` | LRU cache size for directory-analysis results. |
| `APTU_CODER_DISK_CACHE_DIR` | `$XDG_DATA_HOME/aptu-coder/analysis-cache` | Directory for the L2 on-disk call-graph cache used by `analyze_symbol`. Created automatically if it does not exist. |
| `APTU_CODER_DISK_CACHE_DISABLED` | unset | Set to `1` to disable the L2 disk cache entirely. |
| `APTU_CODER_FILE_CACHE_CAPACITY` | `100` | LRU cache size for file-analysis results. |
| `APTU_CODER_METRICS_EXPORT_FILE` | unset | Absolute path for a one-shot JSONL metrics export on shutdown. |
| `APTU_CODER_PORT` | unset | Port for streamable HTTP mode. Equivalent to `--port N`; `--port` takes precedence. When unset and `--port` is not passed, stdio mode is used. |
| `APTU_CODER_BEARER_TOKEN` | unset | Bearer token for Streamable HTTP transport authentication. A warning is logged if the value is fewer than 32 characters. |
| `APTU_SHELL` | unset | Shell for `exec_command`. Defaults to `bash` then `/bin/sh`. |

## Observability

For the JSONL schema, OTel configuration, and span attribute policy, see:

- [OBSERVABILITY.md](https://github.com/clouatre-labs/aptu-coder/blob/main/OBSERVABILITY.md) (repository root)
- [docs/METRICS.md](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/METRICS.md)

## Documentation

- **[AGENTS.md](https://github.com/clouatre-labs/aptu-coder/blob/main/AGENTS.md)** - Contributor reference: project structure, commands, rmcp footguns, tool parameter constraints
- **[ARCHITECTURE.md](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/ARCHITECTURE.md)** - Design goals, module map, data flow, language handler system, caching strategy
- **[CONTRIBUTING.md](https://github.com/clouatre-labs/aptu-coder/blob/main/CONTRIBUTING.md)** - Development workflow, commit conventions, PR checklist
- **[DESIGN-GUIDE.md](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/DESIGN-GUIDE.md)** - Design decisions, rationale, and replication guide for building high-performance MCP servers
- **[MCP Best Practices](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/MCP-BEST-PRACTICES.md)** - Best practices for agentic loops, orchestration patterns, MCP tool design, memory management, and safety controls
- **[METRICS.md](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/METRICS.md)** - Metrics schema, JSONL format, and retention policy
- **[ROADMAP.md](https://github.com/clouatre-labs/aptu-coder/blob/main/docs/ROADMAP.md)** - Development history and future direction
- **[SECURITY.md](https://github.com/clouatre-labs/aptu-coder/blob/main/SECURITY.md)** - Security policy and vulnerability reporting

## License

Apache-2.0. See [LICENSE](https://github.com/clouatre-labs/aptu-coder/blob/main/LICENSE) for details.