feat: complete issue-facade capability enhancement and project cleanup

- Update TODO.md to reflect completed issue-facade capability fixes
- Archive old CLI structure files that were moved to capabilities/issue-facade
- Reorganize remaining CLI components into issue_tracker/ package
- Add test coverage for issue #166 substack theme implementation
- Update document manager and markdown command plugins with latest improvements
- Complete project reorganization following capability-based architecture

This commit finalizes the issue-facade capability enhancement project and
ensures the main repository reflects the current state of all completed work.

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

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

markitect/clean_document_manager.py

@@ -263,11 +263,16 @@ class CleanDocumentManager:
             }}"""
 
         # Heading styles
+        heading_font_style = ""
+        if 'heading_font_family' in props and props['heading_font_family']:
+            heading_font_style = f"font-family: {props['heading_font_family']};"
+
         heading_css = ""
         if props['heading_style'] == 'underlined':
             heading_css = f"""
             h1, h2, h3, h4, h5, h6 {{
                 color: {props['heading_color']};
+                {heading_font_style}
                 border-bottom: 1px solid {props['border_color']};
                 padding-bottom: 0.3em;
             }}"""
@@ -275,6 +280,7 @@ class CleanDocumentManager:
             heading_css = f"""
             h1, h2, h3, h4, h5, h6 {{
                 color: {props['heading_color']};
+                {heading_font_style}
                 margin-top: 2rem;
                 margin-bottom: 1rem;
             }}
@@ -288,6 +294,7 @@ class CleanDocumentManager:
             heading_css = f"""
             h1, h2, h3, h4, h5, h6 {{
                 color: {props['heading_color']};
+                {heading_font_style}
             }}"""
 
         # Text alignment