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.

How it fits together

flowchart LR
    A["AI Agent<br/>(Claude Code / Kimi / Cursor)"] -->|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

Doc	What's in it
`docs/QUICKSTART.md`	Five-minute tour
`docs/USER_MANUAL.md`	Operator + agent manual
`docs/ARCHITECTURE.md`	How and why — design rationale
`docs/TECHNICAL.md`	Source-level internals
`docs/FEDERATION.md`	Multi-repo operating guide
`docs/REPOS_YAML.md`	`repos.yaml` schema
`docs/query-language.md`	`query_graph` ops-array reference
`docs/quickstart-tools.md`	All MCP tools
`docs/command-center.md`	Command Center SPA
`docs/hot-reload.md`	Config hot-reload
`docs/multiplayer.md`	Multi-agent coordination
`docs/hooks.md`	Pre-edit hooks
`docs/INDEX.md`	Docs index

TL;DR

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

# Or non-interactive
curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | \
  bash /dev/stdin --yes

# Configure your project
mkdir -p ~/projects/biller && cd ~/projects/biller
lain repos add auth-svc    https://github.com/acme/auth-svc.git
lain repos add billing-svc https://github.com/acme/billing-svc.git
lain workspaces create biller-core --members auth-svc,billing-svc

# Run the server
lain server --config ./repos.yaml --transport http --port 9999
# Open http://localhost:9999 — that's the Command Center.

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: blast radius for proposed changes, transitive dependency traces, anchor identification, co-change correlation, and contextual build failure decoration so agents can reason about callers rather than just the failing line. Written in Rust, persists across sessions, stays fresh during editing via a file watcher that updates a volatile overlay layered on top of the static graph, and hot-reloads its repos.yaml / workspaces.yaml config without a restart.

The commands

After install, lain exposes these subcommands:

Command	Purpose
`lain server`	Start the MCP server (the headline). Reads `repos.yaml`, serves MCP tools + the Command Center dashboard. Hot-reloads the config when it changes.
`lain mcp`	Single-repo MCP server on stdio. Walks up from cwd for `.git` — the stable "drop in a clone and run" entrypoint. No `repos.yaml` required.
`lain workspaces`	Manage `workspaces.yaml`. Create, list, show, activate (`use`), forget named groups of repos.
`lain repos`	Manage `repos.yaml`. Add, list, remove a repo entry.
`lain query`	Run a `query_graph` ops-array against the project's persisted graph.
`lain oneshot`	One-shot MCP query: boots a transient `lain mcp` server, sends a single `tools/call`, prints the result as a table, and exits. For "just grep the symbols without keeping a server alive".
`lain init`	Scaffold a `repos.yaml` for the current directory. Walks up for `.git`, then writes a minimal config pointing at the discovered workspace.
`lain ask`	Single-user LLM-assisted query (uses `semantic_search` + `explain_symbol` heuristics).
`lain hooks`	Agent pre-edit hook entry point: `claim` / `release` files, `overlap-check` for commit-time symbol overlap, `lock` / `unlock` for the zero-daemon filesystem-fallback layer.
`lain doctor`	"One version of truth" diagnostic. Checks binary version + git SHA, hook script presence, config/hooks dirs (reaping session files older than 30 days), presence registry, and — when `LAIN_URL`/`LAIN_SERVER_URL` is set — both server reachability and the live MCP surface, calling `tools/list` and failing if it errors or advertises zero tools. Exits 0 clean, 1 on a hard failure.
`scripts/demo.sh`	Capability demonstration and benchmark. Boots a real server against a synthetic repo whose call graph is known by construction, checks lain's answers against that ground truth (not merely that it answered), then benchmarks the same tools against this repo at ~3.5k nodes. `--quick` skips the build and benchmark phases; `--json FILE` writes machine-readable results. Exits non-zero if any check fails.

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.

Installation

Quick install (recommended)

curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | bash

The installer downloads the lain binary to ~/.local/lain. After that, configure your agent's MCP config to launch lain server --config ./repos.yaml --transport stdio — see Wire your agent.

Non-interactive install (with options):

# Skip all prompts
curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | \
  bash /dev/stdin --yes

# Download ONNX model for semantic search (all-MiniLM-L6-v2, ~120MB)
curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | \
  bash /dev/stdin --download-model --yes

After installation:

# Reload your shell (the installer adds to ~/.zshrc or ~/.bashrc)
source ~/.zshrc   # or ~/.bashrc

# Verify
lain --version

# Show the available commands
lain --help

Homebrew

brew tap spuentesp/lain https://github.com/spuentesp/lain
brew install lain

# Run the server for your project
lain server --config ./repos.yaml

Build from Source

git clone https://github.com/spuentesp/lain.git
cd lain
cargo build --release    # requires Rust 1.75+

# Binary at ./target/release/lain

Quick Start

1. Install

curl -fsSL https://raw.githubusercontent.com/spuentesp/lain/main/install.sh | bash

2. Configure your project

A project is a directory containing repos.yaml (and optionally workspaces.yaml).

mkdir -p ~/projects/biller && cd ~/projects/biller
lain repos add auth-svc    https://github.com/acme/auth-svc.git
lain repos add billing-svc https://github.com/acme/billing-svc.git
lain workspaces create biller-core --members auth-svc,billing-svc

3. Run the server

lain server --config ./repos.yaml --transport http --port 9999
# Open http://localhost:9999 in your browser for the Command Center.

4. Wire your agent

Add the following to your agent's MCP config (URL/format depends on the agent). The single-repo form is the recommended default — it walks up from the working directory for .git, no repos.yaml needed:

{
  "mcpServers": {
    "lain": {
      "command": "lain",
      "args": ["mcp"]
    }
  }
}

If you want the federation tool surface (list_repos, search_org, get_cross_repo_blast_radius) too, point at a repos.yaml instead:

{
  "mcpServers": {
    "lain": {
      "command": "lain",
      "args": ["server", "--config", "./repos.yaml", "--transport", "stdio"]
    }
  }
}

That's it. The next time your agent starts, it sees the workspace (single-repo form) or the federation, the active workspace, and the full MCP tool surface.

Kimi users: Kimi's plugin security model pins the MCP subprocess cwd to the plugin root, so a naive lain mcp invocation would walk up from the plugin directory instead of your project. As of 0.6.1, lain mcp reads /proc/$PPID/cwd on Linux (the parent agent's cwd) before falling back to its own cwd, so the same {"command":"lain","args":["mcp"]} config works under Kimi with no wrapper. If you're pinned to 0.6.0, ship src/cli/kimi_plugin_wrapper.sh from the source tree and point the plugin manifest at it — the wrapper does the same /proc/$PPID/cwd lookup outside the binary. macOS is unsupported in either path.

Command Center

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).

Multi-project

A project is a directory containing repos.yaml (and optionally workspaces.yaml). Each project has its own server: change to the project directory and run lain server --config ./repos.yaml, or keep multiple servers running on different ports. The Command Center shows recently-used projects in the sidebar with a Copy restart cmd button that copies the right lain server --config <path> --workspace <name> line to the clipboard.

Workspaces are scoped to a single project. Pick one with lain workspaces use <name>; the active name is written to ~/.config/lain/active_workspace and is honored at server start via --workspace auto.

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.

Requirements

Requirement	Details
Rust (build only)	1.75 or newer
Git	Required for co-change analysis
ONNX Model	Optional — for `semantic_search`

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 returns "unavailable" but all other features work.

MCP Transport Modes

Mode	Command	Use Case
`stdio`	`--transport stdio`	Claude Code, MCP clients
`http`	`--transport http --port 9999`	Command Center dashboard + curl-driven MCP

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

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?

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, which means "not in this graph", not "does not exist".

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.

Name		Name	Last commit message	Last commit date
.github		.github
Formula		Formula
docs		docs
hooks		hooks
npm-shim		npm-shim
proptest-regressions/tools		proptest-regressions/tools
scripts		scripts
src		src
tests		tests
toolchains		toolchains
.dockerignore		.dockerignore
.gitignore		.gitignore
CHANGELOG.md		CHANGELOG.md
Cargo.lock		Cargo.lock
Cargo.toml		Cargo.toml
LICENSE		LICENSE
README.md		README.md
build.rs		build.rs
install.sh		install.sh
server.json		server.json

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LAIN-mcp

How it fits together

Documentation

TL;DR

What is Lain?

The commands

Installation

Quick install (recommended)

Homebrew

Build from Source

Quick Start

1. Install

2. Configure your project

3. Run the server

4. Wire your agent

Command Center

Hot Reload

Multi-project

Federation mode

Key Features

Query Language (`query_graph`)

Dependency Intelligence

Architectural Analysis

Search

Code Health

Project Management

Requirements

Optional: Semantic Search

MCP Transport Modes

Troubleshooting

License

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LAIN-mcp

How it fits together

Documentation

TL;DR

What is Lain?

The commands

Installation

Quick install (recommended)

Homebrew

Build from Source

Quick Start

1. Install

2. Configure your project

3. Run the server

4. Wire your agent

Command Center

Hot Reload

Multi-project

Federation mode

Key Features

Query Language (query_graph)

Dependency Intelligence

Architectural Analysis

Search

Code Health

Project Management

Requirements

Optional: Semantic Search

MCP Transport Modes

Troubleshooting

License

About

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Query Language (`query_graph`)