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_tool_path_teaching.py

@@ -1,7 +1,7 @@
 """Phase 72 E2E (Playwright, mock-only): the ls-teaching
 self-correction loop through the real UI.
 
-Story: ``.agent/user_stories/agent-document-tools.md`` (this phase
+Story: ``.agents/user_stories/agent-document-tools.md`` (this phase
 repairs the model-facing contract the phase-70 tools reshaped — the
 2026-09-03 incident: the harness-prior ``ls(path='.')`` misuse met the
 terse refusal, and the model re-reasoned the same paragraphs over and