Fix update command and installer logic (#339)

This change fixes several issues with the `update` command and the
installer:
- Corrects the `update` command logic in `setup/cli/commands/update.py`.
- Fixes the `update` logic in `setup/core/installer.py` to correctly
handle re-installation of components.
- Corrects the installation of MCP servers in `setup/components/mcp.py`.

setup/cli/commands/update.py

@@ -19,7 +19,7 @@ from ...utils.ui import (
 )
 from ...utils.environment import setup_environment_variables
 from ...utils.logger import get_logger
-from ... import DEFAULT_INSTALL_DIR, PROJECT_ROOT
+from ... import DEFAULT_INSTALL_DIR, PROJECT_ROOT, DATA_DIR
 from . import OperationBase
 
 
@@ -275,7 +275,7 @@ def display_update_plan(components: List[str], available_updates: Dict[str, Dict
     print()
 
 
-def perform_update(components: List[str], args: argparse.Namespace) -> bool:
+def perform_update(components: List[str], args: argparse.Namespace, registry: ComponentRegistry) -> bool:
     """Perform the actual update"""
     logger = get_logger()
     start_time = time.time()
@@ -284,10 +284,6 @@ def perform_update(components: List[str], args: argparse.Namespace) -> bool:
         # Create installer
         installer = Installer(args.install_dir, dry_run=args.dry_run)
         
-        # Create component registry
-        registry = ComponentRegistry(PROJECT_ROOT / "setup" / "components")
-        registry.discover_components()
-        
         # Create component instances
         component_instances = registry.create_component_instances(components, args.install_dir)
         
@@ -384,6 +380,9 @@ def run(args: argparse.Namespace) -> int:
     operation = UpdateOperation()
     operation.setup_operation_logging(args)
     logger = get_logger()
+
+    from setup.cli.base import __version__
+
     # ✅ Inserted validation code
     expected_home = Path.home().resolve()
     actual_dir = args.install_dir.resolve()
@@ -457,7 +456,7 @@ def run(args: argparse.Namespace) -> int:
                     return 0
         
         # Perform update
-        success = perform_update(components, args)
+        success = perform_update(components, args, registry)
         
         if success:
             if not args.quiet:

setup/components/mcp.py

@@ -229,7 +229,7 @@ class MCPComponent(Component):
                 ["claude", "mcp", "list"], 
                 capture_output=True, 
                 text=True, 
-                timeout=30,
+                timeout=60,
                 shell=(sys.platform == "win32")
             )
             
@@ -382,7 +382,7 @@ class MCPComponent(Component):
                     ["claude", "mcp", "list"],
                     capture_output=True,
                     text=True,
-                    timeout=15,
+                    timeout=60,
                     shell=(sys.platform == "win32")
                 )
                 
@@ -542,7 +542,7 @@ class MCPComponent(Component):
                 ["claude", "mcp", "list"],
                 capture_output=True,
                 text=True,
-                timeout=30,
+                timeout=60,
                 shell=(sys.platform == "win32")
             )
             

setup/core/installer.py

@@ -28,7 +28,9 @@ class Installer:
         self.install_dir = install_dir or DEFAULT_INSTALL_DIR
         self.dry_run = dry_run
         self.components: Dict[str, Component] = {}
-        self.installed_components: Set[str] = set()
+        from ..services.settings import SettingsService
+        settings_manager = SettingsService(self.install_dir)
+        self.installed_components: Set[str] = set(settings_manager.get_installed_components().keys())
         self.updated_components: Set[str] = set()
 
         self.failed_components: Set[str] = set()
@@ -202,8 +204,8 @@ class Installer:
 
         component = self.components[component_name]
 
-        # Skip if already installed
+        # Skip if already installed and not in update mode
-        if component_name in self.installed_components:
+        if component_name in self.installed_components and not config.get("update_mode"):
             return True
 
         # Check prerequisites
@@ -309,8 +311,10 @@ class Installer:
             self.logger.info("All components validated successfully!")
         else:
             self.logger.error("Some components failed validation. Check errors above.")
+
     def update_components(self, component_names: List[str], config: Dict[str, Any]) -> bool:
         """Alias for update operation (uses install logic)"""
+        config["update_mode"] = True
         return self.install_components(component_names, config)