feat: reorganize capabilities directory structure for better separation

- Move issue-facade submodule from root to capabilities/ directory
- Update .gitmodules to reflect new submodule path: capabilities/issue-facade
- Update all documentation references to new capability paths
- Update agent definitions with new issue-facade location
- Establish logical organization: capabilities/ for all external dependencies
- Maintain wiki/ at root as project documentation, not reusable capability

Improves separation between:
- Project infrastructure (wiki/ at root)
- Reusable capabilities (capabilities/ directory)
- Internal code (markitect/ directory)

🤖 Generated with [Claude Code](https://claude.ai/code)

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

agents/agent-requirements-engineering.md

@@ -117,7 +117,7 @@ python tools/requirements_engineering_toolkit.py validate-mocks --test-file test
 # Enhanced Makefile targets
 issue-start: validate-requirements
 	# Use issue-facade for issue management
-	cd issue-facade && python -m cli.main show $(NUM)
+	cd capabilities/issue-facade && python -m cli.main show $(NUM)
 
 validate-requirements:
 	python tools/requirements_engineering_toolkit.py analyze
@@ -456,7 +456,7 @@ validate-requirements:
 
 issue-start: validate-requirements
 	# Use issue-facade for issue management
-	cd issue-facade && python -m cli.main show $(NUM)
+	cd capabilities/issue-facade && python -m cli.main show $(NUM)
 ```
 
 ### Tool Dependencies