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- init resolves the agent tool (--tool flag > manifest on repair > interactive pick pre-filled by marker detection > claude-code) and materializes template skills under the profile's skill root (.claude/skills, .agents/skills, ...); the chosen tool is recorded in instance.json so update knows where to propose skill diffs - update works zone by zone: .bench-kit/ replaced wholesale (staged swap, manifest survives version-bumped), workflows and skills synced into the working tree as an uncommitted proposal reviewed via git diff, company content never touched; clean-worktree gate keeps the proposal reviewable - template skill source auto-detects the planned .agents/skills migration Co-authored-by: Claude Fable 5 <noreply@anthropic.com>