Docs sync: update all references to v0.4.0 state (52 skills, 9 hooks, 36 templates)

- README: badges and skills section updated (37→52 skills, 8→9 hooks, 29→36 templates); all 52 commands listed in 10 categories; log-agent-stop.sh added to hooks table
- UPGRADING: added complete v0.3.0→v0.4.0 section with file lists, feature highlights, and after-upgrade steps
- WORKFLOW-GUIDE: full rewrite from 10-phase to 7-phase structure; all 52 skills documented across phases and Appendix B
- skills-reference: added 15 missing skills; reorganized into categorized sections
- hooks-reference: added log-agent-stop.sh entry
- quick-start: corrected counts; removed stale orphan doc references
- COLLABORATIVE-DESIGN-PRINCIPLE: AskUserQuestion integration count 10→16

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

docs/COLLABORATIVE-DESIGN-PRINCIPLE.md

@@ -685,4 +685,4 @@ This principle has been fully embedded across the project:
 - **All skills** — Updated to require approval before writing
 - **WORKFLOW-GUIDE.md** — Rewritten with collaborative examples
 - **README.md** — Clarifies collaborative (not autonomous) design
-- **AskUserQuestion tool** — Integrated into 10 skills for structured option UI
+- **AskUserQuestion tool** — Integrated into 16 skills for structured option UI