Fix MCP server: create separate McpServer instance per session

Previously shared one McpServer instance across all sessions/transports,
which caused Protocol._transport to be overwritten when new sessions
connected. This broke message routing for requests on previous transports
after long-running SSE streams.

Now creates a new McpServer instance per session, following the stateful
session pattern from the MCP SDK documentation. Each session gets its own
server+transport pair, preventing transport reference conflicts.

Fixes issue where get_agent_status would fail after wait_for_agent completed.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

packages/server/src/server/agent/providers/claude-agent.ts

@@ -491,6 +491,9 @@ class ClaudeAgentSession implements AgentSession {
       permissionMode: this.currentMode,
       agents: this.defaults?.agents,
       canUseTool: this.handlePermissionRequest,
+      stderr: (data: string) => {
+        console.error("[ClaudeAgentSDK]", data.trim());
+      },
       ...this.config.extra?.claude,
     };