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>

CAPABILITY_INCLUSION_GUIDE.md

@@ -75,7 +75,7 @@ markitect/cli/           # CLI framework capability
 #### 1. **Submodule Capabilities** (Independent Repositories)
 - **Pattern**: Git submodules pointing to external repositories
 - **Benefits**: Independent versioning, separate development, easy updates
-- **Examples**: `issue-facade/`, `wiki/`
+- **Examples**: `capabilities/issue-facade/`, `wiki/`
 
 #### 2. **Local Extracted Capabilities** (Previously Internal, Now Separated)
 - **Pattern**: Moved to `capabilities/` directory but still in this repo
@@ -125,7 +125,7 @@ Extract capability → Choose inclusion pattern → Update registries
 Internal → markitect/issues/ (internal issue management)
 Evaluation → Self-contained, reusable, independent development needed
 Extraction → coulomb/issue-facade (separate repository)
-Inclusion → issue-facade/ (submodule capability)
+Inclusion → capabilities/issue-facade/ (submodule capability)
 Registration → CAPABILITY_REGISTRY.md updated
 ```
 
@@ -146,11 +146,11 @@ markitect/                    # Core repository
 
 ### External Capabilities (4 documented in CAPABILITY_REGISTRY.md)
 ```
-issue-facade/                 # Submodule: Universal issue tracking
-wiki/                        # Submodule: Documentation
 capabilities/
+├── issue-facade/            # Submodule: Universal issue tracking
 ├── markitect-content/       # Local: Content processing
 └── markitect-utils/         # Local: Utility functions
+wiki/                        # Submodule: Documentation
 [External dependencies: click, pytest, sqlalchemy, ...]
 ```