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_l5_infrastructure_database_queries.py

@@ -44,7 +44,7 @@ class TestQueryCommand:
         Issue #14: SQL query interface with safety constraints
         """
         # Test that the main query command exists and is callable
-        result = self.runner.invoke(cli, ['query', '--help'])
+        result = self.runner.invoke(cli, ['db-query', '--help'])
         assert result.exit_code == 0
         assert 'query' in result.output.lower()
         assert 'execute sql query' in result.output.lower() or 'sql' in result.output.lower()
@@ -64,7 +64,7 @@ class TestQueryCommand:
                 {'id': 1, 'filename': 'test.md', 'created_at': '2025-09-25'}
             ]
 
-            result = self.runner.invoke(cli, ['query', 'SELECT * FROM markdown_files LIMIT 1'])
+            result = self.runner.invoke(cli, ['db-query', 'SELECT * FROM markdown_files LIMIT 1'])
 
             assert result.exit_code == 0
             assert 'test.md' in result.output
@@ -85,7 +85,7 @@ class TestQueryCommand:
         ]
 
         for dangerous_sql in dangerous_queries:
-            result = self.runner.invoke(cli, ['query', dangerous_sql])
+            result = self.runner.invoke(cli, ['db-query', dangerous_sql])
             assert result.exit_code != 0
             assert ('not allowed' in result.output.lower() or
                     'allowed' in result.output.lower() or
@@ -106,7 +106,7 @@ class TestQueryCommand:
             # Mock empty result
             mock_db_instance.execute_query.return_value = []
 
-            result = self.runner.invoke(cli, ['query', 'SELECT * FROM markdown_files WHERE id = -1'])
+            result = self.runner.invoke(cli, ['db-query', 'SELECT * FROM markdown_files WHERE id = -1'])
 
             assert result.exit_code == 0
             assert 'no results' in result.output.lower() or len(result.output.strip()) == 0
@@ -124,7 +124,7 @@ class TestQueryCommand:
             # Mock SQL error
             mock_db_instance.execute_query.side_effect = Exception("SQL syntax error")
 
-            result = self.runner.invoke(cli, ['query', 'SELECT * FROM nonexistent_table'])
+            result = self.runner.invoke(cli, ['db-query', 'SELECT * FROM nonexistent_table'])
 
             assert result.exit_code != 0
             assert 'error' in result.output.lower()
@@ -143,7 +143,7 @@ class TestSchemaCommand:
 
         Issue #14: Schema inspection commands
         """
-        result = self.runner.invoke(cli, ['schema', '--help'])
+        result = self.runner.invoke(cli, ['db-schema', '--help'])
         assert result.exit_code == 0
         assert 'schema' in result.output.lower()
         assert ('database' in result.output.lower() or
@@ -173,7 +173,7 @@ class TestSchemaCommand:
                 }
             }
 
-            result = self.runner.invoke(cli, ['schema'])
+            result = self.runner.invoke(cli, ['db-schema'])
 
             assert result.exit_code == 0
             assert 'markdown_files' in result.output
@@ -198,11 +198,11 @@ class TestSchemaCommand:
             mock_db_instance.get_schema.return_value = mock_schema
 
             # Test JSON format
-            result = self.runner.invoke(cli, ['schema', '--format', 'json'])
+            result = self.runner.invoke(cli, ['db-schema', '--format', 'json'])
             assert result.exit_code == 0
 
             # Test YAML format
-            result = self.runner.invoke(cli, ['schema', '--format', 'yaml'])
+            result = self.runner.invoke(cli, ['db-schema', '--format', 'yaml'])
             assert result.exit_code == 0
 
 
@@ -346,7 +346,7 @@ class TestQuerySafety:
 
         for operation in write_operations:
             query = f"{operation} markdown_files"
-            result = runner.invoke(cli, ['query', query])
+            result = runner.invoke(cli, ['db-query', query])
 
             # Should be rejected
             assert result.exit_code != 0 or 'not allowed' in result.output.lower()
@@ -364,7 +364,7 @@ class TestQueryTemplates:
         runner = CliRunner()
 
         # Test that templates or examples are shown in help
-        result = runner.invoke(cli, ['query', '--help'])
+        result = runner.invoke(cli, ['db-query', '--help'])
         assert result.exit_code == 0
 
         # Should mention examples or templates
@@ -393,5 +393,5 @@ class TestQueryTemplates:
             ]
 
             for query in common_queries:
-                result = runner.invoke(cli, ['query', query])
+                result = runner.invoke(cli, ['db-query', query])
                 assert result.exit_code == 0