Fix agent shutdown lifecycle: no-op shutdown, orphaned LS processes, missing MCP cleanup

Three related bugs preventing proper cleanup of language server processes:

1. SerenaAgent.shutdown() checked `hasattr(self, "_is_initialized")` but that
   attribute was never set, making shutdown always return early (no-op).
   Replace with `hasattr(self, "_active_project")` which is set early in
   __init__ and correctly guards against __del__ on partial construction.

2. _activate_project() replaced self._active_project without shutting down
   the previous project first, orphaning its language server processes.
   Now calls old_project.shutdown() before switching.

3. MCP server_lifespan() logged "shutting down" but never called
   agent.shutdown(), so language servers were orphaned on MCP server exit.
   Now calls agent.shutdown() in a try/finally block.

src/serena/agent.py

@@ -699,6 +699,11 @@ class SerenaAgent:
                 f"(2) Configure one MCP server per backend in your client."
             )
 
+        # shut down the previously active project to release its language server processes
+        if self._active_project is not None:
+            log.info(f"Shutting down previously active project '{self._active_project.project_name}' before switching")
+            self._active_project.shutdown()
+
         self._active_project = project
         project.set_agent(self)
 
@@ -845,7 +850,8 @@ class SerenaAgent:
         """
         Shuts down the agent, freeing resources and stopping background tasks.
         """
-        if not hasattr(self, "_is_initialized"):
+        # guard against __del__ being called on a partially constructed instance
+        if not hasattr(self, "_active_project"):
             return
         log.info("SerenaAgent is shutting down ...")
         if self._active_project is not None:

src/serena/mcp.py

@@ -341,8 +341,12 @@ class SerenaMCPFactory:
         openai_tool_compatible = self.context.name in ["chatgpt", "codex", "oaicompat-agent"]
         self._set_mcp_tools(mcp_server, openai_tool_compatible=openai_tool_compatible)
         log.info("MCP server lifetime setup complete")
-        yield
-        log.info("MCP server shutting down")
+        try:
+            yield
+        finally:
+            log.info("MCP server shutting down")
+            if self.agent is not None:
+                self.agent.shutdown()
 
     def _get_initial_instructions(self) -> str:
         assert self.agent is not None