CLI reference

Both binaries expose the same commands: agent-scaffold <command> and scaffold <command>. Bare scaffold with no subcommand opens the interactive shell.

Start here

Command	Purpose
agent-scaffold scaffold [project_dir]	Open the interactive shell (the recommended way to work). With a path, attaches to an existing generated project. See the REPL reference.

Generate

Command	Purpose
agent-scaffold new	Interactive project generator. By default chains into the full lifecycle (generation → up → browser); --no-autorun, --no-open-browser, --non-interactive opt out. Supports --bundle, --obs-hosting, --effort, --model, --write-mode, and source overrides.
agent-scaffold regenerate <project> <file>	Re-prompt the model for a single file in an existing project.
agent-scaffold validate <project> --tier static\|build\|smoke	Re-run a post-generation validation tier without re-invoking the LLM.
agent-scaffold lint-content	Lint a resolved agent-deployments source against the content-drift rules.

Run and deploy

Command	Purpose
agent-scaffold up [project_dir]	Provision a generated project: install deps, start docker services, prompt for missing API keys, run migrations, seed dev data, run smoke tests, launch the frontend dev server, and (opt-in) commit/push. --plan to preview, --yes for CI, --resume / --retry / --skip / --force / --only for re-runs.
agent-scaffold update [project_dir]	Re-run the recipe and 3-way-merge template changes against your edits. --dry-run previews, --continue finalises after manual conflict resolution.
agent-scaffold deploy --target <t>	Push the project to a cloud provider declared by a host.* capability.
agent-scaffold down --cwd <project>	Stop the local stack: kill the frontend dev server, then docker compose down. -v also removes named volumes (destroys local state; asks for confirmation). Never touches cloud.
agent-scaffold eval --cwd <project>	Run the project's eval suite via the matching eval.* capability's plugin. Exits 1 if the score drops below the stored baseline; --update-baseline persists a new one.
agent-scaffold logs <service> --cwd <project>	Tail container logs. The reserved name frontend tails the dev server's log file at .scaffold/frontend.log. -f/--no-follow, --tail N.

Setup

Command	Purpose
agent-scaffold connect [integration]	Connect a stack option: internal docker or cloud hosted.
agent-scaffold status	Probe every capability the recipe declared and print a health table.
agent-scaffold config	Print the resolved configuration (the API key is masked).
agent-scaffold doctor	Read-only audit of local tools. --recipe <slug> adds auth + per-service rows, --no-probes skips network probes, --timeout N caps each probe, --json for machine output, --explain <topic> opens the matching doc. Never mutates.

auth — manage Anthropic credentials

Command	Purpose
agent-scaffold auth login	Capture an Anthropic key (browser or --no-browser paste flow), validate it, and store it keyring-first.
agent-scaffold auth status	Show the active credential backend, stored credentials (masked), and the resolution order. --json for machine output.
agent-scaffold auth logout	Remove a stored credential from every backend it lives in (--all to wipe everything).
agent-scaffold auth setup-token <name>	Store a long-lived CI token in the mode-0600 file backend (--stdin for piped input).

secrets — survey, store, and purge

Command	Purpose
agent-scaffold secrets list	Inventory every credential the CLI knows about, masked. --json for machine output.
agent-scaffold secrets set <NAME>	Store one project secret in the encrypted vault (prompted, never echoed).
agent-scaffold secrets unset <NAME>	Remove one project secret from the encrypted vault.
agent-scaffold secrets purge	Survey + wipe every stored credential (keyring + file + ./.env.local). --yes for CI; --keep-env-local preserves project secrets.