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>

TODO.md

@@ -12,31 +12,38 @@ The structure organizes **future tasks** by their impact, just as a changelog or
 
 This section is for tasks currently being discussed with or worked on by the coding assistant. These are the ephemeral, flow-of-thought tasks.
 
-**🧪 TESTDRIVE-JSUI CAPABILITY EXTRACTION (2025-11-09) - IN PROGRESS**:
-Safely extracting JavaScript UI framework functionality into a dedicated capability while protecting existing hard-won UI functionality and integrating JavaScript tests into the main Python test suite.
+**🔧 FIX BROKEN ISSUE-FACADE CAPABILITY (2025-11-10) - COMPLETED ✅**:
+Successfully fixed the issue-facade capability by restructuring the package organization to match pyproject.toml expectations.
 
-**📋 Workplan**: [docs/workplan-testdrive-jsui-capability.md](docs/workplan-testdrive-jsui-capability.md)
+**📋 Actions Completed**:
+- [x] Diagnosed package structure mismatch (pyproject.toml expected `issue_tracker` package but code was in flat structure)
+- [x] Fixed module import issue by creating `issue_tracker/` package and moving `cli/`, `core/`, `backends/` into it
+- [x] Verified capability functionality is restored (CLI commands working, package installs correctly)
+- [x] Tested with actual issue access (CLI prompts for backend configuration as expected)
 
-**Current Status**: Implementing Phase 1 - Foundation Setup
-- [ ] Create capability directory structure
-- [ ] Setup pyproject.toml with dependencies
-- [ ] Create package.json with Jest configuration
-- [ ] Implement Python-JavaScript bridge
-- [ ] Create capability Makefile
-- [ ] Write basic README documentation
+**🎨 IMPLEMENT DOCUMENT STYLING (Issue #166) - COMPLETED ✅**:
+Successfully implemented Substack-style document theme for enhanced long-form reading experience.
 
-**Objectives**:
-- 🔒 Zero-risk migration with copy-first approach
-- 🧪 Integrate JavaScript tests into main Python test suite
-- 🏗️ Clean capability architecture for JavaScript framework
-- 📊 Enhanced CI/CD integration for JavaScript testing
-- 🚀 Future extensibility for JavaScript framework evolution
+**📋 Features Implemented**:
+- [x] Substack document theme in layered theme system
+- [x] Spectral serif font for body text (optimized for long-form reading)
+- [x] Lora sans-serif font for headings (clean typography hierarchy)
+- [x] Warm cream background (#FAF9F1) for reduced eye strain
+- [x] Bronze accent color (#b08d57) for visual hierarchy
+- [x] 680px max-width for optimal reading line length
+- [x] 1.6 line-height for comfortable reading
+- [x] Complete TDD test coverage (6/6 tests passing)
+- [x] CLI integration: `markitect md-render --theme substack`
+- [x] Layered theme compatibility with existing mode/UI themes
 
-**Safety Mechanisms**:
-- Copy-first approach (never move until verified)
-- Dual-track testing during migration
-- Gradual integration with rollback options
-- Comprehensive test verification at each step
+**Implementation Details**:
+- Added to `LAYERED_THEMES` as document-scope theme
+- Extended CSS generation to support `heading_font_family` property
+- Maintained backward compatibility with `TEMPLATE_STYLES`
+- Full integration with existing theme system architecture
+
+**🧪 TESTDRIVE-JSUI CAPABILITY EXTRACTION (2025-11-09) - COMPLETED ✅**:
+Successfully extracted JavaScript UI framework functionality into a dedicated capability with complete automated test integration. The capability now provides 68 JavaScript tests + 11 Python integration tests for comprehensive testing coverage.
 
 **🏗️ MAJOR ARCHITECTURE REFACTORING (2025-11-03) - COMPLETED ✅**: Successfully completed comprehensive JavaScript refactoring using Test-Driven Development methodology.