io.github.Ataraxy-Labs/sem MCP Server

Part of the Ataraxy Labs stack — agent-native infrastructure for software development. See also: weave (entity-level git merge driver) · inspect (semantic code review) · opensessions (tmux sidebar for coding agents).

Read the manifesto: https://ataraxy-labs.com/#thesis · Essays: https://ataraxy-labs.com/blogs · LLMs: https://ataraxy-labs.com/llms.txt

<p align="center"> <img src="assets/banner.svg" alt="sem" width="600" /> </p> <p align="center"> <a href="https://trendshift.io/repositories/25348" target="_blank"><img src="https://trendshift.io/api/badge/repositories/25348" alt="Ataraxy-Labs%2Fsem | Trendshift" style="width: 250px; height: 55px;" width="250" height="55"/></a> </p> <p align="center"> <strong>Semantic version control built on Git.</strong><br> Instead of lines changed, sem tells you what entities changed: functions, methods, classes. </p> <p align="center"> <a href="https://ataraxy-labs.com/blogs/code-is-not-text">Why sem?</a> · <a href="#install">Install</a> · <a href="#commands">Commands</a> · <a href="#use-with-ai-agents-mcp">Agents (MCP)</a> · <a href="docs/cloud-consent.html">Cloud consent</a> · <a href="https://github.com/Ataraxy-Labs/sem/releases/latest">Releases</a> </p> <p align="center"> <a href="https://github.com/Ataraxy-Labs/sem/releases/latest"><img src="https://img.shields.io/github/v/release/Ataraxy-Labs/sem?color=blue&label=release" alt="Release"></a> <img src="https://img.shields.io/badge/rust-stable-orange" alt="Rust"> <img src="https://img.shields.io/badge/tests-133_passing-brightgreen" alt="Tests"> <a href="LICENSE"><img src="https://img.shields.io/badge/license-MIT-yellow" alt="License"></a> <img src="https://img.shields.io/badge/languages-31-blue" alt="Languages"> </p>

sem is a semantic version control tool that works on top of Git. It parses your code with tree-sitter, extracts every function, class, and method as an entity, and diffs at the entity level instead of lines. This means you see "function blahh was modified" instead of "lines x-y changed."

It works in any Git repo with no setup.

Cloud-backed queries are opt-in per repo: logging in does not upload a repo or send a query. See the cloud consent flow for the public/private repo states, preview screen, local audit log, and forget controls.

<p align="center"> <img src="assets/terminal.svg" alt="sem diff" width="800" /> </p>

Install

curl -fsSL https://raw.githubusercontent.com/Ataraxy-Labs/sem/main/install.sh | sh

Or via Homebrew:

brew install sem-cli

Or via winget on Windows:

winget install AtaraxyLabs.sem

Or install the npm wrapper into node_modules:

npm install --save-dev @ataraxy-labs/sem

With Bun, trust the package so its postinstall script can download the binary:

bun add -d @ataraxy-labs/sem
bun pm trust @ataraxy-labs/sem

Once installed, update to the latest release any time:

sem update

Or build from source (requires Rust):

cargo install --git https://github.com/Ataraxy-Labs/sem sem-cli

Or grab a binary from GitHub Releases.

Or run via Docker:

docker build -t sem .
docker run --rm -it -u "$(id -u):$(id -g)" -v "$(pwd):/repo" sem diff

Name conflict with GNU Parallel

GNU Parallel ships a sem binary (/usr/bin/sem) as a symlink to parallel. If you have both installed, they'll collide. Run sem --version to check which one you're using. (#77)

Quick fixes:

# Option 1: alias in your shell profile (~/.bashrc, ~/.zshrc)
alias sem="$HOME/.cargo/bin/sem"

# Option 2: make sure cargo bin comes first in PATH
export PATH="$HOME/.cargo/bin:$PATH"

# Option 3: if installed via Homebrew
export PATH="$(brew --prefix)/bin:$PATH"

If you installed via npm/bun, the binary lives in node_modules/.bin/sem and is invoked through npx sem or bunx sem, which avoids the conflict entirely.

Commands

Works in any Git repo. No setup required. Also works outside Git for arbitrary file comparison.

sem stores its SQLite entity cache outside the repository, under the OS cache directory by default. Set SEM_CACHE_DIR=/path/to/cache to override the cache root; repo-local overrides are ignored so cache files do not dirty the working tree.

sem diff

Entity-level diff with rename detection, structural hashing, and word-level inline highlights.

# Semantic diff of working changes
sem diff

# Staged changes only
sem diff --staged

# Specific commit
sem diff --commit abc1234

# Commit range
sem diff --from HEAD~5 --to HEAD

# Verbose mode (word-level inline diffs for each entity)
sem diff -v

# Plain text output (git status style)
sem diff --format plain

# JSON output (for AI agents, CI pipelines)
sem diff --format json

# Markdown output (for PRs, reports)
sem diff --format markdown

# Compare any two files (no git repo needed)
sem diff file1.ts file2.ts

# Read file changes from stdin (no git repo needed)
echo '[{"filePath":"src/main.rs","status":"modified","beforeContent":"...","afterContent":"..."}]' \
  | sem diff --stdin --format json

# Only specific file types
sem diff --file-exts .py .rs

sem impact

Cross-file dependency graph shows what breaks if an entity changes.

# Full impact analysis
sem impact authenticateUser

# Direct dependencies only
sem impact authenticateUser --deps

# Direct dependents only
sem impact authenticateUser --dependents

# Affected tests only
sem impact authenticateUser --tests

# JSON output
sem impact authenticateUser --json

# Disambiguate by file
sem impact authenticateUser --file src/auth.ts

# Include default-excluded paths such as generated, fixture, vendor, benchmark, and build trees
sem impact authenticateUser --no-default-excludes

sem blame

Entity-level blame showing who last modified each function, class, or method.

sem blame src/auth.ts

# JSON output
sem blame src/auth.ts --json

sem log

Track how a single entity evolved through git history.

sem log authenticateUser

# Verbose mode (show content diff between versions)
sem log authenticateUser -v

# Limit commits scanned
sem log authenticateUser --limit 20

# JSON output
sem log authenticateUser --json

With no entity, sem log analyzes recent repo history at the entity level: hotspots (most-changed functions/classes, with author counts) and co-change pairs (entities that repeatedly change in the same commits — "if you touch one, don't forget the other"):

sem log                 # repo hotspots + co-change pairs (last 50 commits)
sem log --limit 200     # deeper history
sem log --file src/auth.ts   # scoped to one file
sem log --json          # full data

sem entities

List all entities under a file or directory path. No path is the same as ..

sem entities

sem entities .

sem entities src/auth.ts

# JSON output
sem entities --json
sem entities src/auth.ts --json

# Include default-excluded paths such as generated, fixture, vendor, benchmark, and build trees
sem entities --no-default-excludes

sem context

Token-budgeted context for LLMs: the entity, its dependencies, and its dependents, fitted to a strict content token budget. When the target signature itself does not fit, JSON output reports target_omitted: true.

sem context authenticateUser

# Custom token budget
sem context authenticateUser --budget 4000

# JSON output
sem context authenticateUser --json

# Include default-excluded paths such as generated, fixture, vendor, benchmark, and build trees
sem context authenticateUser --no-default-excludes

Use as default Git diff

Replace git diff output with entity-level diffs. Agents and humans get sem output automatically without changing any commands.

sem setup

Now git diff shows entity-level changes instead of line-level. No prompts, no agent configuration needed. Everything that calls git diff gets sem output automatically. Also installs a pre-commit hook that shows entity-level blast radius of staged changes.

On macOS and Linux, sem setup also wires sem into your Claude Code sessions (free, local, no login): a warm resident graph so structural queries answer in single-digit milliseconds instead of rebuilding each time, and prompt-time context so the code an agent would otherwise forage for arrives at the start of the turn. It edits ~/.claude/settings.json idempotently, backs it up first, and leaves any hooks you already have untouched.

To disable and go back to normal git diff (also removes the session hooks):

sem unsetup

Entity-level diffs on every pull request

Add the GitHub Action and every PR gets one sticky comment showing which functions, classes, and methods changed — updated in place on each push, and calling out cosmetic-only PRs (formatting/comments) explicitly:

# .github/workflows/entity-diff.yml
name: Entity diff
on: pull_request
permissions:
  contents: read
  pull-requests: write
jobs:
  entity-diff:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: Ataraxy-Labs/sem/action@v0.15.1

No config, no API keys, never fails your build. See action/ for details.

Cloud acceleration (for scale and teams)

Local is always free and, after sem setup, always warm — the resident graph keeps your repo hot on your own machine, so day-to-day queries are instant with no login. You do not pay to make your laptop fast.

Cloud is for what a laptop can't do. On a very large monorepo the first local graph build can take a few seconds; a shared team graph shouldn't be rebuilt per developer; and CI wants the graph without checking anything out. sem login connects those cases to sem cloud, which keeps a warm, pre-built graph for your registered repos and serves the heavy queries from it (on a large repo like deno, an impact query is ~86ms from the cloud vs ~573ms rebuilt locally).

sem login                              # GitHub device flow, one time
sem impact myFunc --file src/foo.rs    # served from the cloud's warm graph

It is fully optional and transparent:

• Not logged in, or the cloud is unreachable? sem computes locally and prints the exact same output. No failures, no difference in results.
• SEM_LOCAL=1 forces local computation even when logged in.
• Small repos see no change, local is already fast. The win is for large codebases where rebuilding the graph each time is the bottleneck.

What it parses

32 programming languages with full entity extraction via tree-sitter:

Language	Extensions	Entities
TypeScript	.ts .tsx .mts .cts	functions, classes, interfaces, types, enums, exports
JavaScript	.js .jsx .mjs .cjs	functions, classes, variables, exports
Python	.py	functions, classes, decorated definitions
Go	.go	functions, methods, types, vars, consts
Rust	.rs	functions, structs, enums, impls, traits, mods, consts
Java	.java	classes, methods, interfaces, enums, fields, constructors
C	.c .h	functions, structs, enums, unions, typedefs
C++	.cpp .cc .hpp	functions, classes, structs, enums, namespaces, templates
C#	.cs	classes, methods, interfaces, enums, structs, properties
Ruby	.rb	methods, classes, modules
PHP	.php	functions, classes, methods, interfaces, traits, enums
Swift	.swift	functions, classes, protocols, structs, enums, properties
Elixir	.ex .exs	modules, functions, macros, guards, protocols
Bash	.sh	functions
Fish	.fish	functions
Lua	.lua	functions (global, local, table, and method forms)
HCL/Terraform	.hcl .tf .tfvars	blocks, attributes (qualified names for nested blocks)
Kotlin	.kt .kts	classes, interfaces, objects, functions, properties, companion objects
Fortran	.f90 .f95 .f	functions, subroutines, modules, programs
Vue	.vue	template/script/style blocks + inner TS/JS entities
XML	.xml .plist .svg .csproj	elements (nested, tag-name identity)
ERB	.erb .html.erb	blocks, expressions, code tags
Svelte	.svelte .svelte.js .svelte.ts	component blocks + rune JS/TS modules
Perl	.pl .pm .t	subroutines, packages
Dart	.dart	classes, mixins, extensions, enums, type aliases, functions
OCaml	.ml .mli	values, modules, types, classes, externals
Scala	.scala .sc .sbt	classes, objects, traits, enums, functions, vals, extensions
Nix	.nix	bindings, inherit declarations
Haskell	.hs	functions, signatures, data types, newtypes, classes, instances, type synonyms
Elm	.elm	value declarations, type aliases, type declarations, port annotations, infix declarations
Clojure	.clj .cljs .cljc	vars, functions, macros, multimethods, protocols, records, types
D	.d .di	modules, functions, classes, structs, interfaces, unions, enums, templates, aliases, unittests
Zig	.zig	functions, tests, variables
SQL	.sql .psql .pgsql .ddl	tables, views, functions, indexes, types, schemas, triggers, sequences

Plus structured data formats:

Format	Extensions	Entities
JSON	.json	properties, objects (RFC 6901 paths)
YAML	.yml .yaml	sections, properties (dot paths)
TOML	.toml	sections, properties
EDN	.edn	top-level map entries (keyword keys)
CSV	.csv .tsv	rows (first column as identity)
Markdown	.md .mdx	heading-based sections

Everything else falls back to chunk-based diffing.

Custom extensions and extensionless files

For files with non-standard extensions, create a .semrc in your project root:

.xyz = cpp
.j = json
.mypy = python

sem also reads .gitattributes patterns (diff= and linguist-language=) if you already have those set up. .semrc takes priority when both define the same extension.

For files with no extension at all, sem detects the language automatically from content (imports, declarations, shebang lines, vim modelines). This covers 19 languages with no config needed.

How matching works

Three-phase entity matching:

1. Exact ID match — same entity in before/after = modified or unchanged
2. Structural hash match — same AST structure, different name = renamed or moved (ignores whitespace/comments)
3. Fuzzy similarity — >80% token overlap = probable rename

This means sem detects renames and moves, not just additions and deletions. Structural hashing also distinguishes cosmetic changes (whitespace, formatting) from real logic changes.

Use with AI agents (MCP)

sem mcp starts a Model Context Protocol server over stdin/stdout. It's not a command you run and read yourself: it's a server your coding agent launches in the background so it can ask sem questions while it works. That's the reason mcp lives alongside the normal commands. The agent gets 6 tools, all entity-level: sem_impact, sem_context, sem_diff, sem_entities, sem_blame, sem_log.

Why an agent wants these: instead of reading whole files and burning tokens, it can ask "what breaks if I change submitOrder" (sem_impact) or "give me just the context to refactor this function" (sem_context) and get a precise answer from the dependency graph.

Add it once, then talk to your agent normally. It calls the tools on its own.

Claude Code:

claude mcp add sem -- sem mcp

Or one command that also installs the skill, so the agent knows when to reach for sem:

npx @ataraxy-labs/sem-skill

Cursor, Claude Desktop, or any client with an mcpServers config:

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

If sem isn't on the agent's PATH, use the absolute path to the binary. No separate install is needed: sem mcp ships in the same binary as every other command.

JSON output

sem diff --format json

{
  "summary": {
    "fileCount": 2,
    "added": 1,
    "modified": 1,
    "deleted": 1,
    "moved": 0,
    "renamed": 0,
    "reordered": 0,
    "binary": 0,
    "orphan": 0,
    "total": 3
  },
  "changes": [
    {
      "entityId": "src/auth.ts::function::validateToken",
      "changeType": "added",
      "entityType": "function",
      "entityName": "validateToken",
      "startLine": 12,
      "endLine": 18,
      "oldStartLine": null,
      "oldEndLine": null,
      "filePath": "src/auth.ts"
    }
  ],
  "binaryChanges": []
}

The named change-type buckets (added, modified, deleted, moved, renamed, reordered) always sum to total. orphan is a cross-cutting metadata count for module-level changes, and those changes are already included in the named change-type buckets.

As a library

sem-core can be used as a Rust library dependency:

[dependencies]
sem-core = { git = "https://github.com/Ataraxy-Labs/sem", version = "0.5" }

Used by weave (semantic merge driver) and inspect (entity-level code review).

Architecture

• tree-sitter for code parsing (native Rust, not WASM)
• git2 for Git operations
• rayon for parallel file processing
• xxhash for structural hashing
• Plugin system for adding new languages and formats

Telemetry

sem collects anonymous usage data: the command name (e.g. diff, impact), CLI version, and operating system. Nothing else — no code, file paths, repo names, or user identity. Events are batched locally and sent in the background, so commands never wait on the network.

Disable it any time:

export SEM_NO_TELEMETRY=1   # or DO_NOT_TRACK=1

Contributing

Want to add a new language? See CONTRIBUTING.md for a step-by-step guide.

Star History

License

MIT OR Apache-2.0