feat: implement plugin-based architecture with md- command prefixes - Issue #44

Complete migration of markdown commands to plugin-based architecture:

✅ Architecture Changes:
- Created comprehensive MarkdownCommandsPlugin with md- prefixes
- Migrated legacy commands: ingest → md-ingest, get → md-get, list → md-list
- Leveraged existing CommandPlugin framework for consistency
- Removed deprecated unprefixed commands from CLI

✅ Backward Compatibility:
- Comprehensive bash aliases (aliases.sh) for smooth transition
- Migration guide with detailed transition instructions
- Convenience functions for common workflows

✅ Test Suite Updates:
- Fixed 107+ core CLI tests to use new command structure
- Updated all test files referencing old commands
- Verified end-to-end functionality with complete test coverage

✅ Benefits Delivered:
- Consistent command namespace (all commands now prefixed)
- Modular plugin architecture enabling future extensions
- Lazy loading capabilities for performance optimization
- Clear separation of concerns for maintainability

Cost: €0.15 for comprehensive architectural improvement

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

tests/test_l4_service_document_modification.py

@@ -5,7 +5,7 @@ This test validates the newly implemented get and modify commands that
 complete Issue #2 requirements for document manipulation and roundtrip validation.
 
 Requirements tested:
-- markitect get command functionality
+- markitect md-get command functionality
 - markitect modify command with --add-section and --update-front-matter
 - AST serialization and roundtrip validation
 - Integration with existing AST cache and database systems
@@ -24,7 +24,7 @@ from markitect.serializer import ASTSerializer
 
 
 class TestGetCommand:
-    """Test suite for markitect get command."""
+    """Test suite for markitect md-get command."""
 
     def setup_method(self):
         """Set up test fixtures."""
@@ -91,14 +91,14 @@ class TestGetCommand:
         ]
 
     def test_get_command_exists(self):
-        """Test that get command is available in CLI."""
-        result = self.runner.invoke(cli, ['get', '--help'])
+        """Test that md-get command is available in CLI."""
+        result = self.runner.invoke(cli, ['md-get', '--help'])
         assert result.exit_code == 0
-        assert 'get' in result.output.lower()
+        assert 'md-get' in result.output.lower()
         assert 'retrieve and output' in result.output.lower()
 
     def test_get_command_retrieves_file(self):
-        """Test that get command can retrieve a processed file."""
+        """Test that md-get command can retrieve a processed file."""
         with tempfile.TemporaryDirectory() as temp_dir:
             cache_dir = Path(temp_dir) / '.ast_cache'
             cache_dir.mkdir()
@@ -133,25 +133,25 @@ class TestGetCommand:
                     with patch('markitect.cli.Path') as path_constructor:
                         path_constructor.return_value = cache_path_mock
 
-                        result = self.runner.invoke(cli, ['get', 'test.md'])
+                        result = self.runner.invoke(cli, ['md-get', 'test.md'])
 
                         assert result.exit_code == 0
                         assert 'Test Document' in result.output
 
     def test_get_command_handles_missing_file(self):
-        """Test that get command handles missing files gracefully."""
+        """Test that md-get command handles missing files gracefully."""
         with patch('markitect.cli.DatabaseManager') as mock_db_mgr:
             mock_db_instance = MagicMock()
             mock_db_mgr.return_value = mock_db_instance
             mock_db_instance.get_markdown_file.return_value = None
 
-            result = self.runner.invoke(cli, ['get', 'nonexistent.md'])
+            result = self.runner.invoke(cli, ['md-get', 'nonexistent.md'])
 
             assert result.exit_code != 0
             assert 'not found in database' in result.output.lower()
 
     def test_get_command_outputs_to_file(self):
-        """Test that get command can output to a file."""
+        """Test that md-get command can output to a file."""
         with tempfile.TemporaryDirectory() as temp_dir:
             output_file = Path(temp_dir) / 'output.md'
             cache_dir = Path(temp_dir) / '.ast_cache'
@@ -183,7 +183,7 @@ class TestGetCommand:
                     mock_file.read.return_value = json.dumps(self.test_ast)
                     mock_open.return_value.__enter__.return_value = mock_file
 
-                    result = self.runner.invoke(cli, ['get', 'test.md', '--output', str(output_file)])
+                    result = self.runner.invoke(cli, ['md-get', 'test.md', '--output', str(output_file)])
 
                     assert result.exit_code == 0
                     assert 'written to' in result.output.lower()