fix(execute): the step loop survives an adversarial review

An independent review of abc3083 found 15 defects, the two worst verified
in scratch repos. Each fix started with a test that failed.

- Proof of red could be "proven" by the environment: a start point
  unpacked with git archive had no node_modules and no .git, so any test
  failed there. The start point is now a git clone --shared checked out at
  start_sha, gitignored top-level entries are linked in, and a control run
  (start point + the change) must pass, or the result is not-run.
- The Test first file was never committed (the template lists it apart
  from Files:) and leaked into the next step's diff. The step's scope is
  now Files: + test files, staged at the checkpoint.
- New files outside Files: were invisible to every check. Every untracked
  file is registered with --intent-to-add; a revert unregisters them.
- The floor guard paired renames (foo.test.js -> .bak read as clean) and
  missed skipIf and node's t.skip/t.todo; prose files no longer count as
  stubs.
- Phase 7.5 audited from the last step's start_sha; it now uses the run's
  session_start_sha.
- The done line is written after the checkpoint and checked with --commit.
- fix_rounds never passes 5; attempts are never reset; re-control keeps
  the spec/quality verdicts and earlier floor-guard rulings; the closed
  stop list maps every existing stop; failed vs stopped made consistent;
  the controller's effort is said, not assumed.

Tests: 1470 (1468 pass, 0 fail, 2 skipped).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

tests/fixtures/jsonl-schemas.md

@@ -22,7 +22,7 @@
 | trekbrief-stats | ts, task, slug, mode, interview_turns, review_iterations, brief_quality, research_topics, auto_research, auto_result, intent_approved, project_dir, order_id, order_claimed_at, order_reason | commands/trekbrief.md (orchestrator-emit Phase 7; order_* added by lib/stats/stats-append.mjs) | trekbrief.md:961-976 | profile, phase_models, profile_source | none |
 | trekresearch-stats | ts, question, mode, scope, engine, slug, project_dir, brief_path, dimensions, dimensions_baseline, dimensions_baseline_preserved, effort, conv_turns, empty_turns, unique_sources, agents_local, agents_external, gemini_used, confidence, contradictions, open_questions | commands/trekresearch.md (orchestrator-emit Stats tracking) | trekresearch.md:634-676 | profile, phase_models, parallel_agents, external_research_enabled, profile_source | none |
 | trekplan-stats | ts, task, mode, slug, brief_path, project_dir, codebase_size, codebase_files, agents_deployed, deep_dives, research_briefs_used, research_scout_used, critic_verdict, guardian_verdict, outcome | commands/trekplan.md (orchestrator-emit Phase 12) | trekplan.md:805-826 | profile, phase_models, parallel_agents, profile_source | none |
-| trekexecute-stats (Phase 9 record) | ts, plan, plan_type, mode, result, steps_total, steps_passed, steps_failed, steps_skipped, failed_at_step | lib/stats/stats-append.mjs (trekexecute.md Phase 9) | trekexecute.md:2263-2285 | profile, phase_models, profile_source | none |
+| trekexecute-stats (Phase 9 record) | ts, plan, plan_type, mode, result, steps_total, steps_passed, steps_failed, steps_skipped, failed_at_step | lib/stats/stats-append.mjs (trekexecute.md Phase 9) | trekexecute.md:2325-2347 | profile, phase_models, profile_source | none |
 | trekexecute-stats (autonomy events) | ts, event, known_event, payload | lib/stats/event-emit.mjs `emit()` | event-emit.mjs:78-99 | payload.profile, payload.phase_models, payload.profile_source | none |
 | trekexecute-stats (PostToolUse Bash) | ts, session_id, command_excerpt, duration_ms, success | hooks/scripts/post-bash-stats.mjs (Bash PostToolUse) | post-bash-stats.mjs:42-54 | none (hook is plugin-level, not profile-aware) | command_excerpt (CWE-212) |
 | trekreview-stats | ts, slug, verdict, counts (BLOCKER/MAJOR/MINOR/SUGGESTION), reviewed_files_count, mode, duration_ms | commands/trekreview.md (orchestrator-emit Phase 8) | trekreview.md:255 | profile, phase_models, profile_source | none |