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>

issue_tracker/cli/__init__.py

@@ -0,0 +1,20 @@
+"""
+CLI presentation layer.
+
+This package handles all CLI-specific concerns:
+- Argument parsing and validation
+- Output formatting and presentation
+- User interaction and feedback
+- Error handling and display
+
+The CLI layer delegates business logic to services and focuses purely on
+presentation and user interface concerns.
+"""
+
+from .core import CLIFramework
+from .presenters import *
+from .commands import *
+
+__all__ = [
+    'CLIFramework'
+]