Native Codex workflow runtime

• Interactive planning workflows must begin in /plan. Gather every material choice there and produce an approved plan without mutating GitHub or project files.
• Continue mutations in a second normal-mode invocation of the same skill, passing the approved plan or .plans/<file> explicitly.
• Refinement is an exception to that two-invocation procedure: an ordinary normal-mode refine invocation asks its material questions, validates the proposal and applies it in the same invocation. refinement.confirmBeforeApply: true adds final review in that invocation; false or absent does not ask again. An explicit /plan refinement remains read-only and returns the proposal for a later normal-mode invocation. skills/refine/codex.md owns the pre-write checks and independent automerge policy.
• Persist phase state at .cenci/checkpoints/<workflow>-<target>.json with node "${PLUGIN_ROOT}/codex/checkpoint.mjs" <init|advance|block|complete|clear> <path> <workflow> <target> <phase>. The helper validates schema version 1 and uses atomic rename. Store workflow, target, phase, plan path, worktree, last completed gate, and status.
• On execution ambiguity, persist the checkpoint, clear the active goal, ask exactly one blocking question, and stop. Resume from the checkpoint after the answer.
• Arm a native Codex goal only after an approved implementation plan enters execution: call create_goal({objective: "Complete approved plan <path> through an open PR"}) after verifying get_goal({}) has no active goal. Clear it before human input/errors and after PR creation with update_goal({status:"complete"}) only when the objective is achieved; otherwise checkpoint and return control so the client clears/pauses the active goal.
• Prefer generated .codex/agents/*.toml roles. If unavailable, delegate to a built-in worker with the same bounded role prompt and report that fallback in the checkpoint.
• Keep authenticated mutations, pushes, PR creation, and user questions in the root agent.