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>

.gitmodules

@@ -2,6 +2,6 @@
 	path = wiki
 	url = http://92.205.130.254:32166/coulomb/markitect_project.wiki.git
 	branch = main
-[submodule "issue-facade"]
-	path = issue-facade
+[submodule "capabilities/issue-facade"]
+	path = capabilities/issue-facade
 	url = http://92.205.130.254:32166/coulomb/issue-facade.git