aigon apply

apply is the one verb you run to bring Aigon into a repository and to keep it current.

cd /path/to/project
aigon apply

On first run (no .aigon/ directory present), apply bootstraps the repo:

• Creates the spec folder structure under docs/specs/ (features, research, feedback with all lane subdirectories)
• Writes docs/specs/README.md
• Ensures .aigon/.board-map.json and .env.local are in .gitignore
• Installs the project pre-commit hook
• Allocates a base port block (on profiles where dev servers are enabled)
• Bootstraps workflow-engine snapshots for any pre-existing specs (seed-clone case)
• Creates ~/.aigon/worktrees/<repo>/ and seeds agent trust

After bootstrap, normal apply logic runs: registers the repo in the global registry, refreshes templates for any installed agents, and writes .aigon/version + .aigon/applied-digest.

On subsequent runs (.aigon/ already present), apply runs only the template-refresh path — no banner, no bootstrap, no next-step hint.

What apply does on a fresh repo

When you run aigon apply in a new Git repo, the output looks like:

✨ First-time setup: bringing Aigon into this repo…
ACTION: Initializing Aigon in ./docs/specs ...
✅ ./docs/specs directory structure created.
…
Next: aigon install-agent cc gg cx cu

The next-step hint lists only the agent CLIs that are already on your PATH.

Flags

Preconditions

• Must be run inside a Git repository (.git/ present). In non-git directories, apply exits non-zero with a clear error.
• Worktrees (.aigon/worktree.json present) skip bootstrap, digest write, version write, and registry write.

Replacing aigon init

aigon init is deprecated. aigon apply replaces it entirely — it handles both first-time initialization and ongoing updates, so there is only one verb to remember.

# Deprecated
aigon init
aigon apply  # separate second step
 
# Current
aigon apply  # one command does both

aigon init still works but prints a deprecation warning. It will be removed in a future release.

See also

• remove — remove Aigon-managed files from a repo
• install-agent — install agent commands, skills, and hooks
• doctor — detect and repair project state drift