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init

Bootstraps a repo end to end: system-doctor preflight, repo analysis (code repos), git hooks, and agent context. Idempotent — re-running reports “Already initialised” and writes nothing.

analyse

Detects the repo’s languages, frameworks, package manager, scripts, and test patterns, writing the result to .tiny-brain/analysis.json (and technology context files under .tiny-brain/tech/).
Agents read analysis.json to run your scripts (npm run test, not an improvised test runner) — re-run analyse after changing the toolchain.

doctor

Toolchain health checks. Exits 0 when everything passes or warns, 1 on any critical. Each failing check prints a copy-pasteable Fix: line.

config

Credentials and preferences. Preferences resolve repo → global → default; show-sources shows which layer each value came from.
Repo preferences live in .tiny-brain/config.json; global ones in ~/.tiny-brain/config/preferences.json. Notable keys: enableTDD, enableQuality, defaultPersona, testPatterns, reviewPipeline, and the directory keys (docsDirectory, prdDirectory, adrDirectory, fixesDirectory). An unknown key errors with the full valid-key list, so get is a safe way to probe.