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Colin provides a command-line interface for managing projects and running compilations. The CLI is designed around a simple workflow: initialize a project, add your documents, and run the compiler.

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init

The colin init command creates a new project: 
colin init
This creates colin.toml and a sample model in the current directory: 
Created:
→ colin.toml
→ models/hello.md

Run `colin run` to compile your project.

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Options

Customize the project during initialization: 
colin init --name my-context --models src/docs --output dist
OptionDescriptionDefault
--nameProject nameDirectory name
--modelsSource documents directorymodels
--outputCompiled output directoryoutput
Non-default values are written to colin.toml. You can also initialize an existing directory: 
cd existing-project
colin init
If colin.toml already exists, the command fails with an error rather than overwriting.

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run

The colin run command compiles your project: 
colin run
See Running the Compiler for detailed documentation on compilation behavior, output interpretation, and flags.

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Quick Reference

colin run                    # Compile changed documents
colin run --no-cache         # Recompile everything
colin run --ephemeral        # Don't write to .colin/ (for testing, CI)
colin run -q                 # Suppress progress output
colin run --output ./out     # Override output directory
colin run --update           # Update outputs from their source project
colin run --var key=value    # Override a variable
colin run --no-banner        # Hide the logo banner
colin run --no-clean         # Skip auto-clean after compilation

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skills

The colin skills command group manages installed skills.

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update

Update all Colin-managed skills in a skills directory: 
colin skills update
By default, this scans ~/.claude/skills/ for subdirectories containing .colin-manifest.json files and updates them in parallel. Specify a different directory: 
colin skills update ~/.codex/skills/
Colin reads each manifest’s source project location, recompiles it, and writes updated outputs back to the skill directory. This keeps all your skills fresh with a single command. Combine with cron or CI to automate skill updates: 
# Update skills every hour
0 * * * * colin skills update -q

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clean

The colin clean command removes stale files from outputs: 
colin clean
Stale files are outputs no longer tracked by the manifest—they appear when you delete or rename model files.

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From a Project

When run from a project directory (with colin.toml), Colin finds the output location and checks for stale files: 
Project: my-context
Output:  output/

Will remove stale files:
  output/old-report.md
  output/renamed-doc.md

Continue? (y/N)

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From an Output Directory

Colin can also clean output directories directly. This works with any directory containing Colin manifests: 
cd ~/.claude/skills
colin clean
Colin scans for .colin-manifest.json files and groups stale files by project: 
Will remove stale files:

[team-context]
  team-context/old-doc.md

[deployment-guide]
  deployment-guide/deprecated.md

Continue? (y/N)
Each manifest defines its own scope—Colin only removes files the manifest tracks. Multiple skill projects can coexist in the same directory safely.

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Ignore Patterns

Colin ignores common system files by default (.DS_Store, Thumbs.db, etc.). For additional patterns, create a .colinignore file in your output directory: 
# .colinignore - gitignore-style patterns
*.bak
scratch/
temp-*

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Include Cache

Use --all to also remove stale files from .colin/compiled/: 
colin clean --all
This checks both output/ and .colin/compiled/ for stale files. Your manifest and LLM call history remain intact—only orphaned compiled artifacts are removed.

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Skip Confirmation

Use -y or --yes to skip the confirmation prompt: 
colin clean -y
colin clean --all -y

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Auto-Clean

By default, colin run and colin update automatically clean stale files after compilation. Skip this with --no-clean: 
colin run --no-clean
colin update --no-clean

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mcp

The colin mcp command group manages MCP server configuration. MCP servers connect Colin to external data sources like project trackers, databases, and APIs.

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add

Add an MCP server to your project: 
# Stdio server (local process)
colin mcp add github uvx mcp-server-github

# With additional arguments
colin mcp add linear npx -y @linear/mcp-server

# With environment variables
colin mcp add postgres npx @anthropic/mcp-server-postgres -e DATABASE_URL=postgres://...

# HTTP/SSE server (remote)
colin mcp add remote-api https://api.example.com/mcp --transport http
The first argument is the server name you’ll use in templates. The second is the command (for stdio) or URL (for http/sse).
OptionDescription
-t, --transportTransport type: stdio, sse, or http
-e, --envEnvironment variables in KEY=VALUE format
Transport defaults to stdio for commands and http for URLs.

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list

View configured servers: 
colin mcp list
Output: 
┌────────┬───────┬─────────────────────────────┐
│ Name   │ Type  │ Connection                  │
├────────┼───────┼─────────────────────────────┤
│ github │ stdio │ uvx mcp-server-github       │
│ linear │ stdio │ npx -y @linear/mcp-server   │
└────────┴───────┴─────────────────────────────┘

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remove

Remove a server from configuration: 
colin mcp remove github

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test

Verify a server connection works: 
colin mcp test github
Colin starts the server, connects to it, and lists available resources: 
Testing connection to github...
✓ Connected to github

Resources (3):
  repo://owner/repo/readme - Repository README
  repo://owner/repo/issues - Open issues
  repo://owner/repo/pulls - Pull requests
Use this to discover what resources a server provides before referencing them in your documents.

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auth

Manage OAuth authentication for MCP providers like Linear and Notion. 
colin mcp auth clear      # Clear all OAuth tokens
colin mcp auth clear -f   # Skip confirmation
This removes cached OAuth tokens, requiring re-authentication on next use. Useful when experiencing authentication errors (401s, 500s) or when you need to switch accounts. Tokens are stored at ~/.colin/mcp-oauth/. Clearing tokens affects all providers that use OAuth.

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Project Resolution

Colin finds your project by searching for colin.toml starting from the current directory and walking up parent directories. This lets you run commands from any subdirectory: 
cd my-project/models/products
colin run  # Finds colin.toml in my-project/
Most commands accept a --project option to specify a different project directory: 
colin run --project /path/to/other-project

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Exit Codes

Colin uses standard exit codes:
CodeMeaning
0Success
1Error (compilation failed, project not found, etc.)
In scripts, check the exit code to determine success: 
if colin run -q; then
    echo "Compilation succeeded"
else
    echo "Compilation failed"
    exit 1
fi