Summary

--worktree is currently exposed in CLI/API but does not create or run loops in a dedicated git worktree. For Phase 4/S5 parallel loops (and outcomes expected from #39 / #59), real worktree isolation is a prerequisite.

Part of #59.
Supports #39, #71, #72.

Problem

Current behavior indicates a gap between contract and implementation:

• wiggum run --worktree forwards the flag, but loop execution stays in the project root working tree.
• feature-loop.sh parses --worktree and logs it, but does not git worktree add or switch APP_DIR to a per-feature worktree.
• TUI run path does not pass --worktree today, so interactive runs cannot use isolation.
• Review prompt text still references worktree cleanup despite no guaranteed worktree creation in the flow.

This weakens reliability for parallelism and can cause branch/working-tree contention.

Scope

• Implement true per-feature worktree provisioning in loop runtime.
• Route all execution contexts consistently:
  • CLI wiggum run --worktree
  • Agent runLoop(worktree=true)
  • TUI run path (configurable or default policy)
• Standardize worktree path strategy and lifecycle:
  • create if missing
  • reuse on --resume
  • deterministic cleanup policy after completion/merge/failure
• Ensure commands run against worktree app dir (tests, build, diff, PR/review gates).
• Align prompt instructions with actual harness ownership (no phantom cleanup steps in prompts).
• Add tests covering flag plumbing + runtime behavior.

Acceptance Criteria

• Running with --worktree creates/uses a dedicated worktree path for the feature branch
• Concurrent loops on different features can run without branch switching conflicts
• --resume reattaches to the same worktree for that feature
• Cleanup behavior is explicit and deterministic (documented + tested)
• TUI run path supports worktree mode consistently with CLI/agent behavior
• Prompt text no longer claims cleanup steps that are not guaranteed by harness

Suggested Labels / Priority

• Type: bug (contract says isolation exists, runtime does not honor it)
• Domains: cli, infrastructure
• Meta: loop, user-facing
• Priority: P1
• Size: M/L