fix(mcp): correct hot-reload sync on default Agent

agent/protocol/agent_stream.py

@@ -594,6 +594,15 @@ class AgentStreamExecutor:
         turns = self._identify_complete_turns()
         logger.info(f"Sending {len(messages)} messages ({len(turns)} turns) to LLM")
 
+        # Pull in any MCP tools that finished loading since this turn started.
+        # Cheap dict reconciliation (microseconds) — lets the agent pick up
+        # newly available MCP tools mid-conversation without a session restart.
+        try:
+            from agent.tools import ToolManager
+            ToolManager().sync_mcp_into_agent(self)
+        except Exception as e:
+            logger.debug(f"[Agent] MCP sync skipped: {e}")
+
         # Prepare tool definitions (OpenAI/Claude format)
         tools_schema = None
         if self.tools:

agent/tools/tool_manager.py

@@ -64,6 +64,13 @@ class ToolManager:
             # server_name -> "pending" / "ready" / "failed"
             # Useful for UI / introspection while async loading is in progress.
             self._mcp_status: dict = {}
+        if not hasattr(self, '_mcp_signature'):
+            # (mtime, sha256) of mcp.json the last time we loaded.
+            # Used by refresh_mcp_if_changed() to skip re-parsing when nothing changed.
+            self._mcp_signature: tuple = (None, None)
+        if not hasattr(self, '_mcp_active_configs'):
+            # server_name -> normalized config dict, for diff-based reload.
+            self._mcp_active_configs: dict = {}
 
     def load_tools(self, tools_dir: str = "", config_dict=None):
         """
@@ -257,6 +264,31 @@ class ToolManager:
         except Exception as e:
             logger.error(f"Error configuring tools from config: {e}")
 
+    def _mcp_json_path(self) -> str:
+        import os
+        workspace = os.path.expanduser(conf().get("agent_workspace", "~/cow"))
+        return os.path.join(workspace, "mcp.json")
+
+    def _read_mcp_json_signature(self):
+        """
+        Return (mtime, sha256_of_bytes) for ~/cow/mcp.json without parsing.
+        Returns (None, None) if the file doesn't exist or is unreadable.
+        Cheap enough (one stat + one small read) to call on every agent init.
+        """
+        import os
+        import hashlib
+        path = self._mcp_json_path()
+        try:
+            mtime = os.path.getmtime(path)
+        except OSError:
+            return (None, None)
+        try:
+            with open(path, "rb") as f:
+                digest = hashlib.sha256(f.read()).hexdigest()
+        except OSError:
+            return (mtime, None)
+        return (mtime, digest)
+
     def _load_mcp_configs(self) -> list:
         """
         Load MCP server configs with priority:
@@ -266,8 +298,7 @@ class ToolManager:
         import os
         import json as _json
 
-        workspace = os.path.expanduser(conf().get("agent_workspace", "~/cow"))
+        mcp_json_path = self._mcp_json_path()
-        mcp_json_path = os.path.join(workspace, "mcp.json")
 
         if os.path.exists(mcp_json_path):
             try:
@@ -298,6 +329,12 @@ class ToolManager:
             if self._mcp_loaded:
                 return
             mcp_servers_config = self._load_mcp_configs()
+            # Snapshot the signature now so future refresh_mcp_if_changed()
+            # calls can short-circuit when nothing has changed on disk.
+            self._mcp_signature = self._read_mcp_json_signature()
+            self._mcp_active_configs = {
+                cfg.get("name", "<unnamed>"): cfg for cfg in mcp_servers_config
+            }
             if not mcp_servers_config:
                 # Mark as loaded even when there is nothing to load,
                 # so we don't re-read the config file on every call.
@@ -322,6 +359,88 @@ class ToolManager:
                 f"({len(mcp_servers_config)} server(s) configured)"
             )
 
+    def refresh_mcp_if_changed(self):
+        """
+        Cheap check whether ~/cow/mcp.json has changed since last load.
+        If it has, do a diff-based reload: start newly added servers,
+        shut down removed ones, and restart any whose config was edited.
+        Untouched servers are left running.
+
+        Designed to be called on every agent creation. The fast path is
+        a single os.stat() — completely free when nothing has changed.
+        """
+        with self._mcp_lock:
+            new_sig = self._read_mcp_json_signature()
+            if new_sig == self._mcp_signature:
+                return  # no-op fast path
+
+            try:
+                new_configs = self._load_mcp_configs()
+            except Exception as e:
+                logger.warning(f"[ToolManager] MCP reload — failed to parse config: {e}")
+                return
+
+            new_by_name = {
+                cfg.get("name", "<unnamed>"): cfg for cfg in new_configs
+            }
+            old_by_name = self._mcp_active_configs
+
+            added = [n for n in new_by_name if n not in old_by_name]
+            removed = [n for n in old_by_name if n not in new_by_name]
+            changed = [
+                n for n in new_by_name
+                if n in old_by_name and new_by_name[n] != old_by_name[n]
+            ]
+
+            if not (added or removed or changed):
+                # Signature drifted but content is logically identical
+                # (e.g. user re-saved the file without edits). Just sync.
+                self._mcp_signature = new_sig
+                return
+
+            logger.info(
+                f"[ToolManager] mcp.json changed — "
+                f"adding={added}, removing={removed}, restarting={changed}"
+            )
+
+            # Tear down removed + changed servers (changed ones get restarted below)
+            for name in removed + changed:
+                self._teardown_mcp_server(name)
+
+            # Spin up newly added + changed servers in the background
+            to_start = [new_by_name[n] for n in added + changed]
+            if to_start:
+                for cfg in to_start:
+                    self._mcp_status[cfg.get("name", "<unnamed>")] = "pending"
+                threading.Thread(
+                    target=self._load_mcp_tools_async,
+                    args=(to_start,),
+                    daemon=True,
+                    name="mcp-loader-reload",
+                ).start()
+
+            self._mcp_active_configs = new_by_name
+            self._mcp_signature = new_sig
+
+    def _teardown_mcp_server(self, server_name: str):
+        """Shut down one MCP server and drop its tools from the registry."""
+        if self._mcp_registry is None:
+            return
+        client = None
+        with self._mcp_registry._registry_lock:
+            client = self._mcp_registry._clients.pop(server_name, None)
+        if client is not None:
+            try:
+                client.shutdown()
+            except Exception as e:
+                logger.warning(f"[MCP] Error shutting down '{server_name}': {e}")
+        # Drop tools that belonged to this server.
+        for tool_name in list(self._mcp_tool_instances.keys()):
+            tool = self._mcp_tool_instances.get(tool_name)
+            if tool is not None and getattr(tool, "server_name", None) == server_name:
+                self._mcp_tool_instances.pop(tool_name, None)
+        self._mcp_status.pop(server_name, None)
+
     def _load_mcp_tools_async(self, mcp_servers_config):
         """
         Background worker: bring up each MCP server one-by-one and
@@ -374,7 +493,7 @@ class ToolManager:
                     logger.warning(f"[MCP] Server '{server_name}' load failed: {e}")
 
             ready = sum(1 for s in self._mcp_status.values() if s == "ready")
-            total = len(mcp_servers_config)
+            total = len(self._mcp_status)
             logger.info(
                 f"[ToolManager] MCP loading complete: "
                 f"{ready}/{total} server(s) ready, "
@@ -387,6 +506,64 @@ class ToolManager:
         """Return {server_name: status} snapshot for UI / debugging."""
         return dict(self._mcp_status)
 
+    def sync_mcp_into_agent(self, agent) -> tuple:
+        """
+        Reconcile a live agent's tool collection with the current MCP tool registry.
+
+        Adds tools that finished loading after the agent was created,
+        and removes tools whose MCP server was torn down. Built-in tools
+        on the agent are left untouched.
+
+        Handles both representations CowAgent uses:
+          - Agent.tools: list[BaseTool]               (default Agent class)
+          - AgentStream.tools: dict[str, BaseTool]    (streaming agent)
+
+        Returns (added_names, removed_names) for logging.
+        """
+        if agent is None or not hasattr(agent, "tools"):
+            return ([], [])
+
+        from agent.tools.mcp.mcp_tool import McpTool
+        current = self._mcp_tool_instances
+        registry_names = set(current.keys())
+
+        agent_tools = agent.tools
+
+        if isinstance(agent_tools, dict):
+            agent_mcp_names = {
+                name for name, tool in agent_tools.items()
+                if isinstance(tool, McpTool)
+            }
+            added = registry_names - agent_mcp_names
+            removed = agent_mcp_names - registry_names
+            if not (added or removed):
+                return ([], [])
+            for name in added:
+                agent_tools[name] = current[name]
+            for name in removed:
+                agent_tools.pop(name, None)
+
+        elif isinstance(agent_tools, list):
+            agent_mcp_names = {
+                t.name for t in agent_tools if isinstance(t, McpTool)
+            }
+            added = registry_names - agent_mcp_names
+            removed = agent_mcp_names - registry_names
+            if not (added or removed):
+                return ([], [])
+            if removed:
+                agent.tools = [
+                    t for t in agent_tools
+                    if not (isinstance(t, McpTool) and t.name in removed)
+                ]
+            for name in added:
+                agent.tools.append(current[name])
+
+        else:
+            return ([], [])
+
+        return (sorted(added), sorted(removed))
+
     def create_tool(self, name: str) -> BaseTool:
         """
         Get a new instance of a tool by name.

bridge/agent_bridge.py

@@ -462,6 +462,12 @@ class AgentBridge:
                         except Exception as e:
                             logger.warning(f"[AgentBridge] Failed to clear DB after recovery: {e}")
             
+            # Post-message hot-reload: detect edits to ~/cow/mcp.json and
+            # sync any new/removed MCP tools into the live agent in the
+            # background. Off the critical path so user latency is unaffected;
+            # changes take effect on the user's next message.
+            self._schedule_mcp_hot_reload(agent)
+
             # Check if there are files to send (from send/read tool)
             if hasattr(agent, 'stream_executor') and hasattr(agent.stream_executor, 'files_to_send'):
                 files_to_send = agent.stream_executor.files_to_send
@@ -494,6 +500,31 @@ class AgentBridge:
                     logger.warning(f"[AgentBridge] Failed to clear DB after error: {db_err}")
             return Reply(ReplyType.ERROR, f"Agent error: {str(e)}")
     
+    def _schedule_mcp_hot_reload(self, agent):
+        """
+        Fire-and-forget: detect mcp.json edits and reconcile the agent's
+        tool dict in the background. Runs after the user's reply is sent,
+        so any cost (file stat, hash, server boot) never adds to user latency.
+        Failures are isolated and never raise into the message pipeline.
+        """
+        import threading
+        from agent.tools import ToolManager
+
+        def _run():
+            try:
+                tm = ToolManager()
+                tm.refresh_mcp_if_changed()
+                added, removed = tm.sync_mcp_into_agent(agent)
+                if added or removed:
+                    logger.info(
+                        f"[AgentBridge] Agent tools synced — "
+                        f"added={added}, removed={removed}"
+                    )
+            except Exception as e:
+                logger.warning(f"[AgentBridge] MCP hot-reload failed (non-fatal): {e}")
+
+        threading.Thread(target=_run, daemon=True, name="mcp-hot-reload").start()
+
     def _create_file_reply(self, file_info: dict, text_response: str, context: Context = None) -> Reply:
         """
         Create a reply for sending files