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/core.py

@@ -0,0 +1,28 @@
+"""
+CLI framework core.
+
+Provides the main CLI framework and command delegation.
+"""
+
+from typing import Any
+from .commands import ConfigCommands
+
+
+class CLIFramework:
+    """Main CLI framework that delegates to command classes."""
+
+    def __init__(self) -> None:
+        self.config = ConfigCommands()
+
+    # Configuration operations
+    def show_config(self, show_sensitive: bool = False) -> None:
+        return self.config.show_config(show_sensitive)
+
+    def validate_config(self, verbose: bool = False) -> None:
+        return self.config.validate_config(verbose)
+
+    def troubleshoot_config(self) -> None:
+        return self.config.troubleshoot_config()
+
+    def check_config_files(self) -> None:
+        return self.config.check_config_files()