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_l4_service_document_management.py

@@ -262,12 +262,12 @@ class TestIssue4CLIIntegration:
         """Test that the CLI schema command exists and is properly configured."""
         from markitect.cli import cli
 
-        # Check that 'schema' command is registered
-        assert 'schema' in cli.commands
+        # Check that 'db-schema' command is registered
+        assert 'db-schema' in cli.commands
 
         # Verify the command has the expected attributes
-        schema_command = cli.commands['schema']
-        assert schema_command.name == 'schema'
+        schema_command = cli.commands['db-schema']
+        assert schema_command.name == 'db-schema'
         assert schema_command.help is not None