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Refactor handle_persist_flow to use find_eval_protocol_dir for experi… #909

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Job	Run time
Lint & Type Check	1m 14s
MCP End-to-End Tests	51s
Core Tests (Python 3.10)	3m 35s
Batch Evaluation Tests	1m 20s
Core Tests (Python 3.12)	3m 53s
Core Tests (Python 3.11)	3m 43s
Upload Coverage	0s
	14m 36s