LAIN-mcp

LAIN builds a map of how all the code in your project connects — what calls what, what depends on what, which files tend to change together. Then it lets your AI coding assistant ask questions about that map. So instead of the AI just looking at one file and guessing, it can ask "if I change this function, what else breaks?" and get a real answer. It plugs into any AI agent that supports MCP and runs in the background while you work.

See it run

Download MP4 · Download WebM

• Federation overview, repo health, and the call graph — answered in well under a second.
• Edit repos.yaml from the Repos tab; the server hot-reloads without dropping a request.
• Try any MCP tool straight from the Tools tab; Copy as cURL hands the agent a shareable snippet.

[!NOTE] The hero GIF is large (~4 MB) so it autoplays inline on GitHub. For sharper playback, the MP4 and WebM siblings sit alongside it in docs/screenshots/.

How it fits together

flowchart LR
    A["AI Agent<br/>(Claude Code / Kimi / Agy / Codex)"] -->|MCP<br/>JSON-RPC| L["lain"]
    L -->|reads| FS[".lain/<br/>graph.bin"]
    L -->|runs| ENG["LSP / NLP / git<br/>engines"]
    L -->|answers| T["MCP tools<br/>(get_blast_radius,<br/>explain_symbol, …)"]
    A --> T

lain is a long-running MCP server that indexes your code once and keeps it fresh while you work. The agent speaks MCP (JSON-RPC over stdio or HTTP); the server answers structural questions across one repo (lain mcp) or many repos (lain server --config repos.yaml).

Documentation

TL;DR — install in 30 seconds

# Install (interactive — adds `lain` to PATH)
curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | bash

# Reload your shell, then verify
source ~/.zshrc   # or ~/.bashrc
lain --version

See QUICKSTART.md for the full install matrix (Homebrew, build-from-source, non-interactive flags, ONNX model).

What is Lain?

Lain is a persistent code-intelligence MCP server. The headline is lain server: a long-running process that reads a repos.yaml config, indexes every registered repository (locally, by clone, or by shallow fetch), and answers structural questions across them through MCP tools. The server also serves a Command Center dashboard at GET / for humans who want to inspect the federation, edit the config, run queries, and exercise the MCP tool surface directly.

The value over LSP-only or RAG-based approaches is cross-file structural reasoning: agents can ask about blast radius, transitive dependency traces, anchor identification, co-change correlation, and contextual build failure decoration, so they reason about callers rather than just the failing line. Written in Rust, persists across sessions, and hot-reloads its repos.yaml / workspaces.yaml config without a restart.

The commands

After install, lain exposes these subcommands:

The cut surface (agents, hook, projects, top-level use) is gone — those concerns are reached through the commands above. server plus the two config CLIs (workspaces, repos) cover everything the prior surface did, scoped to a single project directory that owns a repos.yaml.

This table is checked against lain --help by tests/cli_surface.rs, so it cannot drift from the binary again.

Quick Start

1. Install — see QUICKSTART.md § Install.
2. Configure — see QUICKSTART.md § Federation (multi-repo).
3. Wire your agent — see QUICKSTART.md § Single-repo (recommended default).

Command Center

For a narrated tour of every tab, see command-center.md § Tour.

When lain server runs with --transport http, it serves the Command Center dashboard at GET /. It's a self-contained vanilla-JS SPA that talks back to the running server over the same JSON-RPC endpoint the MCP tools use. No separate API, no auth portal.

Tabs:

• Overview — get_health + get_federation_health in one view.
• Graph — D3 force-directed graph of the active workspace.
• Repos — per-repo table (id, path, health, node/edge counts).
• Query — runs query_graph against the federation.
• Tools — auto-generated MCP tool tester. Calls tools/list, then renders a form per tool by introspecting its inputSchema. Copy as cURL copies a curl -X POST http://localhost:9999/mcp ... snippet to the clipboard.

The status bar in the footer polls every 2 s for get_server_status and get_reload_status so hand-edits to repos.yaml / workspaces.yaml show up live.

See docs/command-center.md for the full walkthrough.

Hot Reload

lain server watches repos.yaml and workspaces.yaml and rebuilds its federation state when they change — no restart needed. Both the notify watcher (for hand-edits) and the CLI (via lain repos add or lain workspaces create) trigger the same ReloadBus.

When you run lain repos add my-repo …, the CLI writes the YAML atomically (write to temp file, then rename), then signals the running server over a Unix socket at ~/.local/lain/run/<repos-stem>.sock. The server's rebuild task diffs the new file against the live federation and applies add / remove operations against FederatedIndex. get_reload_status reports the state (idle / rebuilding / failed); the Command Center status bar shows it live.

See docs/hot-reload.md for the full picture (internals, observability, failure modes, caveats).

Federation mode

For org-wide structural questions — "who else uses this function?", "what depends on this service?" — run lain server --config ./repos.yaml. Federation mode exposes six MCP tools (list_repos, get_repo_info, get_federation_health, search_org, get_cross_repo_blast_radius, get_cross_repo_blast_radius_for_repo) that answer questions spanning repos. See docs/FEDERATION.md for the full guide and docs/REPOS_YAML.md for the config schema.

Key Features

• Federation mode — index N repos and answer org-wide structural questions across them.
• Command Center — vanilla-JS SPA at GET / for human inspection, config editing, query running, and MCP tool testing.
• Hot reload — repos.yaml / workspaces.yaml changes apply without restarting the server.

Query Language (query_graph)

JSON-based ops array for flexible graph traversals:

{
  "ops": [
    { "op": "find", "type": "Function" },
    { "op": "connect", "edge": "Calls", "depth": { "min": 1, "max": 3 } },
    { "op": "filter", "label": "test" },
    { "op": "semantic_filter", "like": "error handling", "threshold": 0.35 },
    { "op": "limit", "count": 10 }
  ]
}

Available ops: find, connect, filter, semantic_filter, group, sort, limit.

Dependency Intelligence

• get_call_chain — Shortest path between two functions.
• get_blast_radius — Everything affected by a change.
• trace_dependency — What a symbol depends on.
• get_coupling_radar — Files that change together.

Architectural Analysis

• find_anchors — Most-called, most-stable symbols (architectural pillars).
• list_entry_points — Find main(), route handlers, app initialization.
• get_context_depth — How far from an entry point (abstraction layers).
• explore_architecture — High-level tree of modules and files.

Search

• semantic_search — Find code by meaning, not just names. Uses local ONNX embeddings with hybrid scoring (cosine similarity + stemmed token-overlap) and shows body excerpts in the response. BGE-small-en-v1.5 is the recommended model (better than MiniLM for technical corpora); use a query prefix to enable BGE-style asymmetric retrieval.

Code Health

• find_dead_code — Potentially unreachable code (filters trait defaults, common names).
• suggest_refactor_targets — High-coupling, low-stability nodes.

Project Management

A project is a directory containing repos.yaml (and optionally workspaces.yaml). Manage it directly with the CLI:

• lain repos add <name> <url> — register a repo in repos.yaml.
• lain repos list — show registered repos.
• lain repos remove <name> — unregister a repo.
• lain workspaces create <name> --members a,b,c — declare a named workspace.
• lain workspaces list — show all workspaces.
• lain workspaces use <name> — activate a workspace (writes ~/.config/lain/active_workspace).
• lain workspaces current — print the active workspace.
• lain workspaces forget <name> — remove a workspace.

Where to go next

• Operate lain for a team → USER_MANUAL.md
• Federation operating guide → FEDERATION.md
• Full MCP tool reference → quickstart-tools.md
• Command Center narrated tour → command-center.md

Requirements

Optional: Semantic Search

For semantic_search to work, you need an ONNX embedding model. The easiest setup uses the provided install script with --download-model. Otherwise, drop a model into .lain/models/:

mkdir -p .lain/models

# Option A: bge-small-en-v1.5 (recommended — better MTEB scores, 384d, ~120MB)
curl -L https://huggingface.co/BAAI/bge-small-en-v1.5/resolve/main/onnx/model.onnx \
  -o .lain/models/model.onnx
curl -L https://huggingface.co/BAAI/bge-small-en-v1.5/resolve/main/tokenizer.json \
  -o .lain/models/tokenizer.json

# Option B: all-MiniLM-L6-v2 (smaller, 384d, ~80MB)
curl -L https://huggingface.co/sentence-transformers/all-MiniLM-L6-v2/resolve/main/onnx/model.onnx \
  -o .lain/models/model.onnx
curl -L https://huggingface.co/sentence-transformers/all-MiniLM-L6-v2/resolve/main/tokenizer.json \
  -o .lain/models/tokenizer.json

Export the model path so the server picks it up:

export LAIN_EMBEDDING_MODEL=$PWD/.lain/models/model.onnx

For BGE-style asymmetric retrieval (better for short queries), set the query prefix in .lain/tuning.toml:

query_prefix = "Represent this sentence for searching relevant passages: "

Without the model, semantic_search is filtered from tools/list entirely. Other features still work. The binary drops the tool rather than advertise one that always says "unavailable".

MCP Transport Modes

The HTTP transport is no longer combined with stdio in a single both mode — start two lain server processes (or use the HTTP transport and exercise tools via curl against /mcp).

Troubleshooting

For first-time setup, see QUICKSTART.md § First aid before reading this section.

Hand-edit not picked up?

The hot-reload watcher is non-recursive and uses atomic rename. Editing the file in place (vim repos.yaml) triggers a notify event within ~1 s. If you've moved the file across directories, save it back into the same directory.

Repo stuck in indexing / degraded / unavailable / missing?

# Check federation health
curl -s -X POST http://localhost:9999/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"get_federation_health","arguments":{}},"id":1}'

The Command Center's Overview tab shows the same numbers in a single view.

Force a reload:

curl -s -X POST http://localhost:9999/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"request_reload","arguments":{}},"id":1}'

View all available tools:

curl -s -X POST http://localhost:9999/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","method":"tools/call","params":{"name":"get_agent_strategy","arguments":{}},"id":1}'

run_build / run_tests fail with "not found"?

The server inherits the environment of whatever launched it, and an editor-launched MCP server usually has no version-manager shims on PATH. lain searches the toolchain's known install locations (rustup, nvm, pyenv, volta, mise, asdf and friends) before giving up, and the error names every way to fix it. To teach it a manager it doesn't know, add program_dirs / program_resolver to that toolchain's profile — see toolchains/README.md.

Answers look stale, or a symbol "doesn't exist" that clearly does?

lain mcp blocks on the first re-index before its stdio loop comes up, so the first tool call after initialize already sees a populated graph (or LAIN_REINDEX_TIMEOUT was exceeded — see below). The legacy "second call works, first doesn't" footgun is gone.

If you still see stale or missing symbols, check get_health:

• Build: tells you the version and git SHA of the process answering, and warns when a newer binary is on disk. An MCP stdio server is spawned once by its client and outlives every rebuild, so it can be older than your source tree — restart the client to pick up a new build.
• Status: reads Degraded ⚠ when the last re-index failed OR timed out, which means "not in this graph", not "does not exist". A timeout banner means LAIN_REINDEX_TIMEOUT (default 300s for the outer startup budget, 60s for the per-repo pipeline under it) was too short for your working tree — raise it past both defaults (LAIN_REINDEX_TIMEOUT=600 covers a tokio-sized repo on a cold cache) and restart.

Two agents not seeing each other?

They must share one workspace. Presence is exchanged through the state file under ~/.local/lain/state/, so agents on the same repo see each other's claims even when each console spawned its own stdio server. list_active_agents and list_occupancy are the quickest check.

Regenerating the demo video

The hero recording above is checked in. Re-record it after any SPA change:

make record-demo

Or: npm run record-demo --prefix tests/js (runs only the Playwright driver; you still need scripts/record-spa-demo.sh for the ffmpeg encoding pass).

For the offline (synthetic) fixture, run make record-demo-small.

License

MIT — Copyright (c) 2026 spuentesp