Refinery project

Read the shared operating rules for authorization,
blocked operations, and completion. Choose only the requested operation below. An explanation
or diagnosis does not authorize setup or repair.

Use the knowledge-refinery CLI for lifecycle changes. Do not hand-edit managed files when the
CLI can perform the operation. Resolve the repository to an absolute PROJECT_ROOT; command
variables stand for concrete values selected by the user or returned by tools, never placeholders.

Explain, inspect, or diagnose

• Explanation: use the relevant section or reference. Do not run local checks unless the question
  depends on the current repository or machine state.
• State check: run knowledge-refinery project status --target "$PROJECT_ROOT" --json and report
  the active vault, project ID, enabled state, and vault_match. A status-only request ends here.
• Diagnosis or repair: inspect status and run knowledge-refinery doctor --target "$PROJECT_ROOT".
  When MCP is available, obtain refinery_info.version and pass it with --mcp-version to doctor.
  Report failed checks and apply only the requested repair using documented CLI commands.
  Version drift blocks refinery writes; continue permitted inspection until it is resolved.
  Do not repeat a successful preflight unless the relevant state changes.

state=disabled is an intentional opt-out. Re-enable only on the user's explicit request or
approval for that transition. Never hand-edit vault_id to bypass a mismatch.

Set up

For repository setup or an active-vault change, read setup.md.

Maintain project metadata

Read the current record with refinery_get_project_metadata, or
knowledge-refinery project metadata show --target "$PROJECT_ROOT" --json when MCP is unavailable.
Update only changed, stable identity or discovery facts. Keep purpose/domain tags lowercase
kebab-case and technology names in technologies; exclude local paths, temporary state, and guesses.

Prefer refinery_update_project_metadata with the current updated_at as expected_updated_at.
Send only changed fields: omission preserves values, while an empty tags or technologies list
clears it. With the CLI, --clear-tags and --clear-technologies are intentional clears.
Read back the result and verify that project_id is unchanged.

Toggle use

• Enable with knowledge-refinery project enable --target "$PROJECT_ROOT" after the authorization
  above. Add --agents only when the user wants automatic operation.
• Disable with knowledge-refinery project disable --target "$PROJECT_ROOT".
• Verify either transition with knowledge-refinery project status --target "$PROJECT_ROOT".

Disable retains .refinery.yaml with enabled: false and all central-vault knowledge. Repository
offboarding does not authorize deleting vault data.