AutoMat

Add, run, or debug uncertainty and confidence estimation in the agent_qwen workflow. Use when integrating structure_recongnition/confidence_estimation.py, generating per-atom/lattice confidence reports, or adding confidence artifacts to agent_qwen harness outputs.

Run and extend the agent_qwen staged STEM image to CIF harness lines. Use when working on agent_qwen_vl_rpc.py, denoise/template-match/STEM-to-CIF orchestration, runtime tool calls, harness state passing, or real/dry-run testing of the legacy AutoMat v1-style agent pipeline.