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>

markitect/cli.py

@@ -756,67 +756,6 @@ def modify(config, file_path, add_section, section_content, section_level, updat
         sys.exit(1)
 
 
-@cli.command()
-@click.argument('sql', type=str)
-@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
-@pass_config
-def query(config, sql, format):
-    """
-    Execute SQL query against the database.
-
-    DEPRECATED: Use 'db-query' instead. This command will be removed in a future version.
-
-    Execute read-only SQL queries to explore and analyze document metadata.
-    Only SELECT and WITH statements are allowed for security.
-
-    SQL: SQL query to execute (SELECT statements only)
-
-    Examples:
-        markitect db-query "SELECT filename, created_at FROM markdown_files"
-        markitect db-query "SELECT COUNT(*) as total FROM markdown_files" --format json
-        markitect db-query "SELECT * FROM markdown_files WHERE filename LIKE '%.md'" --format yaml
-    """
-    # Show deprecation warning (unless in legacy mode)
-    if not LegacyMode.should_suppress_warnings():
-        emit_deprecation_warning(
-            "The 'query' command is deprecated. Please use 'db-query' instead. "
-            "This command will be removed in a future version."
-        )
-
-    try:
-        if config['verbose']:
-            click.echo(f"Executing query: {sql}", err=True)
-
-        db_manager = config['db_manager']
-
-        # Execute the query
-        results = db_manager.execute_query(sql)
-
-        if not results:
-            if format == 'json':
-                click.echo('[]')
-            elif format == 'yaml':
-                click.echo('[]')
-            else:
-                click.echo("No results found.")
-            return
-
-        # Format and display results
-        formatted_output = format_output(results, format)
-        click.echo(formatted_output)
-
-        if config['verbose']:
-            click.echo(f"Query returned {len(results)} result(s)", err=True)
-
-    except ValueError as e:
-        click.echo(f"Query error: {e}", err=True)
-        sys.exit(1)
-    except Exception as e:
-        click.echo(f"Database error: {e}", err=True)
-        if config['verbose']:
-            import traceback
-            click.echo(traceback.format_exc(), err=True)
-        sys.exit(1)
 
 
 @cli.command('db-query')
@@ -873,58 +812,6 @@ def db_query(config, sql, format):
         sys.exit(1)
 
 
-@cli.command()
-@click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')
-@pass_config
-def schema(config, format):
-    """
-    Show database schema and table structure.
-
-    DEPRECATED: Use 'db-schema' instead. This command will be removed in a future version.
-
-    Display the structure of all tables in the database, including
-    column names, types, and constraints.
-
-    Examples:
-        markitect db-schema
-        markitect db-schema --format json
-        markitect db-schema --format yaml
-    """
-    # Show deprecation warning (unless in legacy mode)
-    if not LegacyMode.should_suppress_warnings():
-        emit_deprecation_warning(
-            "The 'schema' command is deprecated. Please use 'db-schema' instead. "
-            "This command will be removed in a future version."
-        )
-
-    try:
-        if config['verbose']:
-            click.echo("Retrieving database schema...", err=True)
-
-        db_manager = config['db_manager']
-
-        # Get schema information
-        schema_info = db_manager.get_schema()
-
-        if not schema_info:
-            click.echo("No tables found in database.")
-            return
-
-        # Format and display schema
-        formatted_output = format_output(schema_info, format)
-        click.echo(formatted_output)
-
-        if config['verbose']:
-            table_count = len(schema_info)
-            click.echo(f"Schema contains {table_count} table(s)", err=True)
-
-    except Exception as e:
-        click.echo(f"Schema error: {e}", err=True)
-        if config['verbose']:
-            import traceback
-            click.echo(traceback.format_exc(), err=True)
-        sys.exit(1)
-
 
 @cli.command('db-schema')
 @click.option('--format', '-f', type=click.Choice(['table', 'json', 'yaml', 'simple']), default=lambda: get_default_format(['table', 'json', 'yaml', 'simple']), help='Output format')