refactor: Remove deprecated query and schema commands and update all tests

- Remove deprecated 'query' command (replaced by 'db-query')
- Remove deprecated 'schema' command (replaced by 'db-schema')
- Remove 4 obsolete tests that tested deprecated functionality
- Update all remaining tests to use new db-prefixed command names
- CLI now has clean, consistent command structure with proper prefixes
- All 478 tests passing after cleanup

This completes the CLI consistency convention implementation where all
subsystem commands follow the "*-stats" pattern and use proper prefixes.

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

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

tests/test_issue_39_db_command_reorganization.py

@@ -78,47 +78,6 @@ class TestIssue39DatabaseCommandReorganization:
             assert 'markdown_files' in result.output
             mock_db_instance.get_schema.assert_called_once()
 
-    def test_old_query_command_shows_deprecation_warning_but_works(self, runner):
-        """
-        Test backward compatibility: old query command works with deprecation warning.
-
-        Issue #39: Backward compatibility requirement
-        """
-        with patch('markitect.cli.DatabaseManager') as mock_db_mgr:
-            mock_db_instance = MagicMock()
-            mock_db_mgr.return_value = mock_db_instance
-            mock_db_instance.execute_query.return_value = [{'count': 3}]
-
-            result = runner.invoke(cli, [
-                'query', 'SELECT COUNT(*) as count FROM markdown_files'
-            ])
-
-            assert result.exit_code == 0
-            # Should work but show deprecation warning
-            assert 'deprecated' in result.output.lower() or 'deprecat' in result.output.lower()
-            assert 'db-query' in result.output
-            mock_db_instance.execute_query.assert_called_once()
-
-    def test_old_schema_command_shows_deprecation_warning_but_works(self, runner):
-        """
-        Test backward compatibility: old schema command works with deprecation warning.
-
-        Issue #39: Backward compatibility requirement
-        """
-        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_schema.return_value = {
-                'markdown_files': {'columns': []}
-            }
-
-            result = runner.invoke(cli, ['schema'])
-
-            assert result.exit_code == 0
-            # Should work but show deprecation warning
-            assert 'deprecated' in result.output.lower() or 'deprecat' in result.output.lower()
-            assert 'db-schema' in result.output
-            mock_db_instance.get_schema.assert_called_once()
 
     def test_db_delete_command_exists_and_requires_confirmation(self, runner, temp_dir):
         """
@@ -270,25 +229,6 @@ class TestIssue39BackwardCompatibility:
     def runner(self):
         return CliRunner()
 
-    def test_existing_scripts_continue_to_work(self, runner):
-        """
-        Test that existing scripts using old command names continue to work.
-
-        Issue #39: Backward compatibility requirement
-        """
-        with patch('markitect.cli.DatabaseManager') as mock_db_mgr:
-            mock_db_instance = MagicMock()
-            mock_db_mgr.return_value = mock_db_instance
-            mock_db_instance.execute_query.return_value = []
-            mock_db_instance.get_schema.return_value = {}
-
-            # Old commands should still work
-            query_result = runner.invoke(cli, ['query', 'SELECT 1'])
-            schema_result = runner.invoke(cli, ['schema'])
-
-            # Both should work (exit code 0) even if they show warnings
-            assert query_result.exit_code == 0
-            assert schema_result.exit_code == 0
 
     def test_no_breaking_changes_to_command_arguments(self, runner):
         """