fix: add MCP tool timeout + running state to prevent silent stall after hub_repo_details (#127)

[parthwhy]

Problem

When running ml-intern headless from CLI, the agent silently stalls
for 5+ minutes after a hub_repo_details tool call with zero progress
output. The user has no way to know if the agent is working or frozen.

Fixes #127

Root Cause

Two overlapping bugs:

1. No timeout on MCP tool calls (agent/core/tools.py)
hub_repo_details is an MCP tool served by huggingface.co/mcp. The
call await self.mcp_client.call_tool(tool_name, arguments) had zero
timeout — if the HF Hub API is slow or rate-limiting, this await hangs
indefinitely, blocking the entire agent loop.

2. No progress event emitted during tool execution (agent/core/agent_loop.py)
After tool_call fires (showing ▸ hub_repo_details in terminal),
_exec_tool went silent until results arrived. No tool_state_change: running event was emitted for non-approval tools, so the CLI showed
nothing for the entire duration of the stall.

Changes

agent/core/tools.py

• Added import asyncio
• Added MCP_TOOL_TIMEOUT = 30 constant (easy to tune)
• Wrapped mcp_client.call_tool() with asyncio.wait_for(timeout=MCP_TOOL_TIMEOUT)
• Added except asyncio.TimeoutError handler that returns a clear error
  message to the agent so it can retry or continue instead of hanging

agent/core/agent_loop.py

• Emit tool_state_change: running event inside _exec_tool immediately
  before call_tool() so the CLI/frontend shows the tool is actively
  executing

Before / After

Before:
▸ hub_repo_details {"repo_ids": ["openai/whisper-small"]}
[5 minutes of silence → user hits Ctrl+C]

After:
▸ hub_repo_details {"repo_ids": ["openai/whisper-small"]} [running]
[if slow]: Tool 'hub_repo_details' timed out after 30s — agent continues

Testing

Reproduced locally with the command from the issue:
ml-intern "Fine-tune a small Whisper model for Arabic speech recognition
on a GPU under 5 dollars and compare the fine-tuned model's metrics to
the original model."
Agent no longer stalls silently after hub_repo_details.

[fglogan]

closed per maintainer request