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/plugins/builtin/markdown_commands.py

@@ -180,6 +180,27 @@ LAYERED_THEMES = {
             'link_hover_color': '#999999'
         }
     },
+    'substack': {
+        'scope': 'document',
+        'properties': {
+            'font_family': 'Spectral, Georgia, "Times New Roman", serif',
+            'heading_font_family': 'Lora, -apple-system, BlinkMacSystemFont, sans-serif',
+            'max_width': '680px',
+            'body_background': '#FAF9F1',
+            'body_color': '#333333',
+            'heading_color': '#333333',
+            'text_align': 'left',
+            'line_height': '1.6',
+            'heading_style': 'simple',
+            'accent_color': '#b08d57',
+            'link_color': '#b08d57',
+            'link_hover_color': '#8b6c42',
+            'code_background': '#f5f4ed',
+            'code_color': '#333333',
+            'blockquote_border': '#b08d57',
+            'blockquote_color': '#666666'
+        }
+    },
 
     # Branding Themes - Company/personal styling
     'corporate': {
@@ -205,7 +226,8 @@ LEGACY_THEME_MAPPING = {
     'basic': ['light', 'standard', 'basic'],
     'github': ['light', 'standard', 'github'],
     'dark': ['dark', 'standard', 'basic'],
-    'academic': ['light', 'standard', 'academic']
+    'academic': ['light', 'standard', 'academic'],
+    'substack': ['light', 'standard', 'substack']
 }
 
 # Keep TEMPLATE_STYLES for backward compatibility in tests
@@ -229,6 +251,11 @@ TEMPLATE_STYLES = {
         'body_color': '#333',
         'font_family': 'Georgia, Times New Roman, serif',
         'max_width': '650px'
+    },
+    'substack': {
+        'body_color': '#333333',
+        'font_family': 'Spectral, Georgia, "Times New Roman", serif',
+        'max_width': '680px'
     }
 }