Standardize on the .agents/ directory (shared with project skills):
phases/, user_stories/, reports/, screenshots/, validate.sh, and
phase-sessions/ + pipeline.log all move to .agents/ (git mv preserves
history; runtime artifacts move alongside).
Updates every reference in AGENTS.md, README.md, .gitignore, app
docstrings, and test story headers. Historical KB content in data/
and the runtime pipeline.log transcript are left untouched.
Remove the blanket .agent/ gitignore so the phase roadmap, user
stories, reports, and PLAN.md are versioned with the code. Only
runtime artifacts (.agent/phase-sessions/, .agent/pipeline.log)
remain ignored. Update AGENTS.md git protocol rule to match.