Retry MCP tool calls after closed-resource errors by refreshing session

[AminMahpour]

Motivation

• Follow-up MCP tool calls in the same chat session were failing with closedResourceError/"resource is closed" due to stale stateful MCP sessions and cached tool objects.

Description

• Added retry handling in invoke_mcp_tool_command to catch closed-resource failures, refresh the MCP session scope, reload tools, and retry the same tool once in deepagent_runtime.py.
• Extended _get_mcp_tools with a refresh flag to allow invalidating the _mcp_tools_cache and rebuilding tool objects on demand.
• Added _refresh_mcp_scope to close/reset the current stateful MCP scope and _is_closed_mcp_resource_error to detect closed-resource error messages.
• The retry path reloads tools for the candidate servers and attempts the tool invocation once more after refreshing state.

Testing

• Ran python -m py_compile deepagent_runtime.py, which completed successfully.

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Codex Task