chore(agent): track .agent/ planning tree in git

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.

AGENTS.md

@@ -27,8 +27,9 @@
 8. **Git protocol:** Git is mandatory. One **atomic, professional commit per
    completed phase** (Conventional Commits, e.g. `feat(rag): stream RAG
    answers over SSE with source citations`). Always append `--no-gpg-sign`
-   (the repo also sets `commit.gpgsign=false`). `.agent/` is gitignored by
-   design — use `git add -f .agent/…` when a commit must record plan changes.
+   (the repo also sets `commit.gpgsign=false`). `.agent/` is **tracked and
+   committed** with the phase — only runtime artifacts (`.agent/phase-sessions/`,
+   `.agent/pipeline.log`) are gitignored.
 9. **Test gates are non-negotiable:** a phase is complete only when unit +
    integration tests pass, `app/` coverage is **>90%**
    (`uv run pytest --cov=app --cov-report=term-missing`), and the phase's