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>

tests/test_issue_166_substack_theme.py

@@ -0,0 +1,183 @@
+"""
+Tests for Issue #166: Document theme that mimics substack fonts and fontsizes
+
+This module tests the implementation of a Substack-style document theme
+for enhanced long-form reading experience.
+"""
+
+import pytest
+import tempfile
+import os
+from pathlib import Path
+from unittest.mock import patch, MagicMock
+import json
+
+# Add project root to path for imports
+import sys
+project_root = Path(__file__).parent.parent
+sys.path.insert(0, str(project_root))
+
+
+class TestIssue166SubstackTheme:
+    """Test Substack theme implementation for long-form reading."""
+
+    def setup_method(self):
+        """Set up test environment."""
+        # Create temporary directory for test outputs
+        self.temp_dir = tempfile.mkdtemp()
+        self.markdown_content = """# The Mythology of Ireland
+
+This is a test document for validating the Substack theme implementation.
+The theme should provide excellent readability for longer essays online.
+
+## Typography and Layout
+
+The Substack style emphasizes:
+- Serif fonts for body text (Spectral)
+- Sans-serif fonts for headings (Lora)
+- Generous line spacing for readability
+- Warm color palette with soft cream background
+
+### Key Design Principles
+
+1. **Readability First**: Typography optimized for long-form content
+2. **Visual Breathing Room**: Generous margins and spacing
+3. **Print-Inspired**: Traditional typographic principles
+4. **Eye Comfort**: Soft, low-contrast color scheme
+
+> "The best interfaces are almost invisible to the user. They don't get in the way of the content."
+> — A design principle that guides Substack's approach
+
+This longer paragraph demonstrates how the theme handles extended body text.
+It should be comfortable to read with appropriate line height, font size,
+and spacing that reduces eye strain during extended reading sessions.
+"""
+
+    def teardown_method(self):
+        """Clean up test environment."""
+        # Clean up temporary files
+        import shutil
+        shutil.rmtree(self.temp_dir, ignore_errors=True)
+
+    def test_substack_theme_available_in_layered_themes(self):
+        """Test that substack theme is available in LAYERED_THEMES - Issue #166."""
+        from markitect.plugins.builtin.markdown_commands import LAYERED_THEMES
+
+        # Substack theme should be available as a document theme
+        assert 'substack' in LAYERED_THEMES
+        substack_theme = LAYERED_THEMES['substack']
+
+        # Should be scoped as a document theme
+        assert substack_theme['scope'] == 'document'
+
+        # Should have required typography properties
+        properties = substack_theme['properties']
+        assert 'font_family' in properties
+        assert 'max_width' in properties
+        assert 'body_background' in properties
+        assert 'heading_font_family' in properties
+
+    def test_substack_theme_typography_properties(self):
+        """Test that substack theme has correct typography properties - Issue #166."""
+        from markitect.plugins.builtin.markdown_commands import LAYERED_THEMES
+
+        substack_theme = LAYERED_THEMES['substack']
+        properties = substack_theme['properties']
+
+        # Should use serif font for body text (Spectral)
+        assert 'Spectral' in properties['font_family']
+
+        # Should use sans-serif for headings (Lora)
+        assert 'Lora' in properties['heading_font_family']
+
+        # Should have appropriate max width for readability
+        max_width = properties['max_width']
+        # Convert to int if it has px suffix
+        if max_width.endswith('px'):
+            width_value = int(max_width[:-2])
+        else:
+            width_value = int(max_width)
+        assert 600 <= width_value <= 750  # Good range for long-form reading
+
+        # Should have warm cream background
+        assert properties['body_background'] == '#FAF9F1'
+
+    def test_substack_theme_legacy_compatibility(self):
+        """Test that substack theme works with legacy TEMPLATE_STYLES - Issue #166."""
+        from markitect.plugins.builtin.markdown_commands import TEMPLATE_STYLES
+
+        # Should be available in legacy template styles for backward compatibility
+        assert 'substack' in TEMPLATE_STYLES
+        substack_legacy = TEMPLATE_STYLES['substack']
+
+        # Should have required legacy properties
+        assert 'body_color' in substack_legacy
+        assert 'font_family' in substack_legacy
+        assert 'max_width' in substack_legacy
+
+    def test_substack_theme_cli_integration(self):
+        """Test Substack theme through CLI md-render command - Issue #166."""
+        input_file = Path(self.temp_dir) / "substack_test.md"
+        input_file.write_text(self.markdown_content)
+
+        output_file = Path(self.temp_dir) / "substack_test.html"
+
+        from markitect.cli import cli
+        from click.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(cli, [
+            'md-render',
+            str(input_file),
+            '--output', str(output_file),
+            '--theme', 'substack'
+        ])
+
+        assert result.exit_code == 0, f"CLI command failed: {result.output}"
+        assert output_file.exists()
+
+        html_content = output_file.read_text()
+
+        # Should contain Substack-specific styling
+        assert 'Spectral' in html_content  # Body font
+        assert 'Lora' in html_content       # Heading font
+        assert '#FAF9F1' in html_content    # Background color
+
+    def test_substack_theme_html_generation(self):
+        """Test HTML generation with Substack theme - Issue #166."""
+        from markitect.plugins.builtin.markdown_commands import generate_html_with_embedded_markdown
+
+        test_markdown = "# Test Article\n\nThis is a test paragraph for the Substack theme."
+        title = "Substack Theme Test"
+
+        html = generate_html_with_embedded_markdown(
+            test_markdown, title, "substack", "", {}
+        )
+
+        # Should generate valid HTML
+        assert '<!DOCTYPE html>' in html
+        assert title in html
+
+        # Should include Substack styling
+        assert 'Spectral' in html  # Body font should be present
+        assert 'Lora' in html      # Heading font should be present
+        assert '#FAF9F1' in html   # Background color should be present
+
+    def test_substack_theme_layered_combination(self):
+        """Test Substack theme combines properly with other layer themes - Issue #166."""
+        from markitect.plugins.builtin.markdown_commands import parse_theme_string, combine_theme_properties
+
+        # Test combining substack document theme with light mode and standard UI
+        theme_list = parse_theme_string("light,standard,substack")
+
+        assert 'light' in theme_list     # Mode theme
+        assert 'standard' in theme_list  # UI theme
+        assert 'substack' in theme_list  # Document theme
+
+        # Should be able to apply layered themes
+        combined_styles = combine_theme_properties(theme_list)
+
+        # Should include properties from all themes
+        assert 'body_background' in combined_styles  # From light theme
+        assert 'editor_panel_bg' in combined_styles  # From standard UI theme
+        assert 'font_family' in combined_styles      # From substack document theme