Fix MCP shutdown after timed-out agent runs

[kamilnowak05]

Summary

• start the MCP event loop inside its worker thread and wait until it is ready before scheduling work
• cancel and drain pending MCP-loop tasks before stopping/closing the loop, preventing destroyed pending subprocess pipe tasks after timeouts
• harden hosted MCP OAuth handling by normalizing confidential client metadata and serializing auth flows across providers

Root cause

A Linear-triggered Hermes agent run hit repeated non-streaming model-call timeouts. During process cleanup, shutdown_mcp_servers() stopped and closed the MCP background loop while stdio MCP subprocess startup/reconnect tasks were still pending. That left asyncio subprocess pipe coroutines half-open and produced the observed BaseSubprocessTransport._connect_pipes / coroutine ignored GeneratorExit warnings.

Tests

• pytest tests/tools/test_mcp_tool.py::TestShutdown tests/tools/test_mcp_oauth_manager.py -q — 14 passed
• pytest tests/tools/test_mcp_tool.py::TestShutdown::test_shutdown_cancels_pending_loop_tasks_before_closing_loop -q — 1 passed
• pytest tests/tools/test_mcp_tool.py -q — 184 passed
• pytest tests/tools/test_mcp_probe.py tests/tools/test_mcp_oauth.py tests/tools/test_mcp_oauth_manager.py tests/tools/test_mcp_oauth_cold_load_expiry.py tests/tools/test_mcp_oauth_metadata.py tests/tools/test_mcp_oauth_bidirectional.py -q — 80 passed, 1 existing warning
• python -m py_compile tools/mcp_tool.py tools/mcp_oauth.py tools/mcp_oauth_manager.py tests/tools/test_mcp_tool.py tests/tools/test_mcp_oauth_manager.py
• git diff --check

Full suite note: pytest -q was also run and reached completion, but the existing repository-wide suite currently reports unrelated failures outside this change area: 100 failed, 22242 passed, 77 skipped, 214 warnings.