chore: reorganize repository structure

- Move docker-compose files to .docker/compose/
- Move docker-entrypoint.sh to .docker/
- Move DOCKER.md to .docker/README.md
- Move 16 implementation docs to docs/implementation/
- Delete test artifacts (block_test.txt, caddy_*.json)
- Update all references in Dockerfile, Makefile, tasks, scripts
- Add .github/instructions/structure.instructions.md for enforcement
- Update CHANGELOG.md

Root level reduced from 81 items to ~35 visible items.

docs/implementation/README.md

@@ -0,0 +1,39 @@
+# Implementation Documentation Archive
+
+This directory contains archived implementation documentation and historical records
+of feature development in Charon.
+
+## Purpose
+
+These documents serve as historical references for:
+
+- Feature implementation details and decisions
+- Migration summaries and upgrade paths
+- Investigation reports and debugging sessions
+- Phase completion records
+
+## Document Index
+
+Documents will be organized here after migration from the project root:
+
+| Document | Description |
+|----------|-------------|
+| `AGENT_SKILLS_MIGRATION_SUMMARY.md` | Agent skills system migration details |
+| `BULK_ACL_FEATURE.md` | Bulk ACL feature implementation |
+| `I18N_IMPLEMENTATION_SUMMARY.md` | Internationalization implementation |
+| `IMPLEMENTATION_SUMMARY.md` | General implementation summary |
+| `INVESTIGATION_SUMMARY.md` | Investigation and debugging records |
+| `ISSUE_16_ACL_IMPLEMENTATION.md` | Issue #16 ACL implementation details |
+| `PHASE_*_COMPLETE.md` | Phase completion documentation |
+| `QA_*.md` | QA audit and verification reports |
+| `SECURITY_*.md` | Security implementation records |
+| `WEBSOCKET_FIX_SUMMARY.md` | WebSocket fix implementation |
+
+## Note
+
+These are **historical implementation records**. For current documentation, refer to:
+
+- `/docs/` - Main documentation
+- `/README.md` - Project overview
+- `/CONTRIBUTING.md` - Contribution guidelines
+- `/CHANGELOG.md` - Version history