feat(autoresearch-agent): fix critical bugs, package as plugin with 5 slash commands
**Bug fixes (run_experiment.py):**
- Fix broken revert logic: was saving HEAD as pre_commit (no-op revert),
now uses git reset --hard HEAD~1 for correct rollback
- Remove broken --loop mode (agent IS the loop, script handles one iteration)
- Fix shell injection: all git commands use subprocess list form
- Replace shell tail with Python file read
**Bug fixes (other scripts):**
- setup_experiment.py: fix shell injection in git branch creation,
remove dead --skip-baseline flag, fix evaluator docstring parsing
- log_results.py: fix 6 falsy-zero bugs (baseline=0 treated as None),
add domain_filter to CSV/markdown export, move import time to top
- evaluators: add FileNotFoundError handling, fix output format mismatch
in llm_judge_copy, add peak_kb on macOS, add ValueError handling
**Plugin packaging (NEW):**
- plugin.json, settings.json, CLAUDE.md for plugin registry
- 5 slash commands: /ar:setup, /ar:run, /ar:loop, /ar:status, /ar:resume
- /ar:loop supports user-selected intervals (10m, 1h, daily, weekly, monthly)
- experiment-runner agent for autonomous loop iterations
- Registered in marketplace.json as plugin #20
**SKILL.md rewrite:**
- Replace ambiguous "Loop Protocol" with clear "Agent Protocol"
- Add results.tsv format spec, strategy escalation, self-improvement
- Replace "NEVER STOP" with resumable stopping logic
**Docs & sync:**
- Codex (157 skills), Gemini (229 items), convert.sh all pick up the skill
- 6 new MkDocs pages, mkdocs.yml nav updated
- Counts updated: 17 agents, 22 slash commands
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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