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-project-management.md

@@ -48,7 +48,7 @@ You are the MarkiTect project assistant, specialized in providing project status
 - **Issue Workflow**: Create → Triage → Plan → Schedule → Implement → Close
 
 **TDD Workflow Management:**
-- For issue management tasks, use the **issue-facade** system located in `issue-facade/`
+- For issue management tasks, use the **issue-facade** system located in `capabilities/issue-facade/`
 - The issue-facade provides unified CLI for GitHub, GitLab, Gitea, and local SQLite backends
 - This includes sidequest management, test planning, and comprehensive development workflow guidance