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/presenters/formatters.py

@@ -0,0 +1,85 @@
+"""
+Output formatting utilities for CLI presentation.
+"""
+
+import sys
+from typing import Any, Dict, List
+
+
+class OutputFormatter:
+    """Handles output formatting and display."""
+
+    @staticmethod
+    def success(message: str) -> None:
+        """Display success message."""
+        print(f"✅ {message}")
+
+    @staticmethod
+    def info(message: str) -> None:
+        """Display info message."""
+        print(f"📋 {message}")
+
+    @staticmethod
+    def warning(message: str) -> None:
+        """Display warning message."""
+        print(f"⚠️  {message}")
+
+    @staticmethod
+    def error(message: str) -> None:
+        """Display error message."""
+        print(f"❌ {message}")
+
+    @staticmethod
+    def header(title: str, separator: str = "=") -> None:
+        """Display section header."""
+        print(title)
+        print(separator * len(title))
+        print()
+
+    @staticmethod
+    def section(title: str) -> None:
+        """Display section title."""
+        print(f"## {title}")
+        print()
+
+    @staticmethod
+    def bullet_point(text: str, indent: int = 0) -> None:
+        """Display bullet point."""
+        prefix = "   " * indent
+        print(f"{prefix}- {text}")
+
+    @staticmethod
+    def key_value(key: str, value: Any, indent: int = 0) -> None:
+        """Display key-value pair."""
+        prefix = "   " * indent
+        print(f"{prefix}{key}: {value}")
+
+    @staticmethod
+    def empty_line() -> None:
+        """Display empty line."""
+        print()
+
+    @staticmethod
+    def exit_with_error(message: str, exit_code: int = 1) -> None:
+        """Display error and exit."""
+        OutputFormatter.error(message)
+        sys.exit(exit_code)
+
+    @staticmethod
+    def format_file_list(files: List[str], title: str = "Files") -> None:
+        """Format and display file list."""
+        print(f"📄 {title} ({len(files)}):")
+        if files:
+            for file in files:
+                print(f"   - {file}")
+        else:
+            print("   - No files found")
+        print()
+
+    @staticmethod
+    def format_command_list(commands: List[str], title: str = "Commands") -> None:
+        """Format and display command list."""
+        print(f"💡 {title}:")
+        for command in commands:
+            print(f"   - {command}")
+        print()