fix(mcp): wire MCP tools into agent and fix env var inheritance

Two bugs found during end-to-end validation with Amap and Chrome DevTools
MCP servers:

1. MCP tools were loaded into ToolManager._mcp_tool_instances but never
   added to the agent's tool list. AgentInitializer._load_tools() only
   iterated tool_classes (built-in tools). Added a second pass to append
   all MCP tool instances.

2. When a MCP server config contains an "env" dict, it was passed directly
   to subprocess.Popen, replacing the entire process environment. This
   caused npx to fail because PATH and other inherited vars were missing.
   Fixed by merging config env on top of os.environ.

Validated with:
- @amap/amap-maps-mcp-server (12 tools, stdio + API key env var)
- chrome-devtools-mcp (29 tools, stdio + remote debugging port)

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

agent/tools/mcp/mcp_client.py

@@ -6,6 +6,7 @@ MCP SDK dependency.
 """
 
 import json
+import os
 import subprocess
 import threading
 import urllib.request
@@ -119,7 +120,8 @@ class McpClient:
             return False
 
         args = self.config.get("args", [])
-        env = self.config.get("env", None)
+        extra_env = self.config.get("env", None)
+        env = {**os.environ, **extra_env} if extra_env else None
 
         self._proc = subprocess.Popen(
             [command] + list(args),