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Refactor handle_persist_flow to use find_eval_protocol_dir for experi… #911

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Job	Run time
Lint & Type Check	1m 4s
Batch Evaluation Tests	1m 7s
Core Tests (Python 3.10)	4m 9s
MCP End-to-End Tests	50s
Core Tests (Python 3.11)	4m 22s
Core Tests (Python 3.12)	4m 31s
Upload Coverage	6s
	16m 9s