auto_agent: Pre-requisites of auto_agent beam search prototype using mock backends

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Several pre-requisites of the beam_search prototype:

1. adk_cli_patch.py: Patches the ADK CLI to defer closing the runner until after session saving, preventing file write failures on shutdown when using MCP filesystem tools.
2. pipeline_agent.py: 1) Turn autotune and profile agent into optional to support a mode of auto_agent which focused on code-correction instead of performance improvement; 2) add a flag to exit the iterations after the auto_agent gets its first valid profile, used by beam search to run short auto_agent sessions.
3. profiling/agent.py: Safely filters out uninitialized tools (e.g. Vertex AI RAG) to prevent agent registration crashes when running in local or restricted environments.
4. profiling/offline_tools.py: Intercepts HLO profiling and xplane trace analysis tools in mock mode to return simulated performance metrics, enabling CPU-only dry-runs without accessing physical TPU trace files.
5. file_tools.py: Adds detailed logging to the restricted_write_file tool to track agent's output file destination