fix(mcp): address PR review feedback on stability and config

Stability fixes in mcp_client.py:
- Fix stderr buffer overflow: start daemon thread to continuously drain
  stderr pipe, preventing 64KB buffer fill that blocks child process
- Fix notification interference: loop readline and skip JSON-RPC messages
  without 'id' field (notifications) instead of treating them as responses
- Fix concurrent race condition: wrap send+receive in _call_lock so
  multiple sessions cannot interleave reads/writes on the same client
- Fix missing timeout: use select.select() with 30s timeout in
  _readline_with_timeout() to prevent infinite block on dead MCP server

Config improvements in tool_manager.py:
- Add _normalize_mcp_configs() to support both list format (mcp_servers)
  and dict format (mcpServers used by Claude Desktop / Cursor)
- Add _load_mcp_configs() to load from ~/cow/mcp.json first, falling back
  to config.json mcp_servers field for backward compatibility

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

agent/tools/mcp/mcp_client.py

@@ -7,6 +7,7 @@ MCP SDK dependency.
 
 import json
 import os
+import select
 import subprocess
 import threading
 import urllib.request
@@ -39,6 +40,7 @@ class McpClient:
         # Shared state
         self._next_id = 1
         self._id_lock = threading.Lock()
+        self._call_lock = threading.Lock()
         self._initialized = False
 
     # ------------------------------------------------------------------
@@ -133,8 +135,26 @@ class McpClient:
             env=env,
         )
         logger.debug(f"[MCP:{self.name}] stdio process started (pid={self._proc.pid})")
+
+        threading.Thread(
+            target=self._drain_stderr, daemon=True, name=f"mcp-stderr-{self.name}"
+        ).start()
+
         return self._handshake()
 
+    def _drain_stderr(self):
+        for line in self._proc.stderr:
+            line = line.strip()
+            if line:
+                logger.debug(f"[MCP:{self.name}] stderr: {line}")
+
+    def _readline_with_timeout(self, timeout: int = 30) -> str:
+        """Read one line from stdio stdout with a hard timeout."""
+        ready, _, _ = select.select([self._proc.stdout], [], [], timeout)
+        if not ready:
+            raise TimeoutError(f"[MCP:{self.name}] stdio read timed out after {timeout}s")
+        return self._proc.stdout.readline()
+
     def _stdio_send(self, message: dict) -> dict:
         """Send a JSON-RPC message over stdio and read the response."""
         raw = json.dumps(message) + "\n"
@@ -142,13 +162,20 @@ class McpClient:
         self._proc.stdin.flush()
 
         while True:
-            line = self._proc.stdout.readline()
+            line = self._readline_with_timeout()
             if not line:
                 raise IOError(f"[MCP:{self.name}] stdio process closed unexpectedly")
             line = line.strip()
             if not line:
                 continue
-            return json.loads(line)
+            try:
+                data = json.loads(line)
+            except json.JSONDecodeError:
+                continue
+            if "id" not in data:
+                logger.debug(f"[MCP:{self.name}] notification skipped: {data.get('method', '?')}")
+                continue
+            return data
 
     # ------------------------------------------------------------------
     # SSE transport
@@ -235,12 +262,13 @@ class McpClient:
 
         message = self._build_request(method, params)
 
-        if self.transport == "stdio":
-            return self._stdio_send(message)
-        elif self.transport == "sse":
-            return self._sse_send(message)
-        else:
-            raise ValueError(f"[MCP:{self.name}] Unsupported transport: {self.transport}")
+        with self._call_lock:
+            if self.transport == "stdio":
+                return self._stdio_send(message)
+            elif self.transport == "sse":
+                return self._sse_send(message)
+            else:
+                raise ValueError(f"[MCP:{self.name}] Unsupported transport: {self.transport}")
 
     def _send_notification(self, method: str, params: dict):
         """Fire-and-forget notification (no response expected)."""

agent/tools/tool_manager.py

@@ -7,6 +7,26 @@ from common.log import logger
 from config import conf
 
 
+def _normalize_mcp_configs(raw) -> list:
+    """
+    Convert MCP server config to internal list format.
+    Supports:
+      - list format (mcp_servers):  [{"name": "x", "type": "stdio", ...}]
+      - dict format (mcpServers):   {"x": {"command": "npx", ...}}
+    """
+    if isinstance(raw, list):
+        return raw
+    if isinstance(raw, dict):
+        result = []
+        for name, cfg in raw.items():
+            entry = {"name": name, **cfg}
+            if "type" not in entry:
+                entry["type"] = "sse" if "url" in entry else "stdio"
+            result.append(entry)
+        return result
+    return []
+
+
 class ToolManager:
     """
     Tool manager for managing tools.
@@ -222,10 +242,35 @@ class ToolManager:
         except Exception as e:
             logger.error(f"Error configuring tools from config: {e}")
 
+    def _load_mcp_configs(self) -> list:
+        """
+        Load MCP server configs with priority:
+          1. ~/cow/mcp.json  (supports both mcpServers and mcp_servers keys)
+          2. config.json mcp_servers field (fallback)
+        """
+        import os
+        import json as _json
+
+        workspace = os.path.expanduser(conf().get("agent_workspace", "~/cow"))
+        mcp_json_path = os.path.join(workspace, "mcp.json")
+
+        if os.path.exists(mcp_json_path):
+            try:
+                with open(mcp_json_path, "r", encoding="utf-8") as f:
+                    data = _json.load(f)
+                raw = data.get("mcpServers") or data.get("mcp_servers") or data
+                logger.info(f"[ToolManager] Loading MCP config from {mcp_json_path}")
+                return _normalize_mcp_configs(raw)
+            except Exception as e:
+                logger.warning(f"[ToolManager] Failed to read {mcp_json_path}: {e}, falling back to config.json")
+
+        raw = conf().get("mcp_servers", [])
+        return _normalize_mcp_configs(raw)
+
     def _load_mcp_tools(self):
         """Load MCP tools from mcp_servers config. Failures are non-fatal."""
         try:
-            mcp_servers_config = conf().get("mcp_servers", [])
+            mcp_servers_config = self._load_mcp_configs()
             if not mcp_servers_config:
                 return