refactor(agents): migrate .agent/ planning tree to .agents/

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.

tests/e2e/test_harness_aligned_tools.py

@@ -1,7 +1,7 @@
 """Phase 70 E2E (Playwright, mock-only): the harness-aligned tool surface
 (``ls`` / ``read(path)`` / ``grep(pattern, path?)``).
 
-Story: ``.agent/user_stories/agent-document-tools.md`` (phase 70 reshapes
+Story: ``.agents/user_stories/agent-document-tools.md`` (phase 70 reshapes
 the tools that story delivered — owner decision 2026-09-03: "match
 existing harnesses as much as possible", the pi.dev tool shapes).
 Run in isolation (DB must be up: ``podman compose up -d db``):