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Refactor dotenv loading to use explicit paths in CLI and API modules #1729

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Run time

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Job	Run time
Lint & Type Check	1m 18s
Batch Evaluation Tests	1m 11s
MCP End-to-End Tests	47s
Core Tests (Python 3.12, Shard 4/4)	2m 5s
Core Tests (Python 3.10, Shard 4/4)	2m 3s
Core Tests (Python 3.11, Shard 3/4)	2m 1s
Core Tests (Python 3.12, Shard 2/4)	5m 1s
Core Tests (Python 3.10, Shard 1/4)	2m 53s
Core Tests (Python 3.10, Shard 3/4)	2m 15s
Core Tests (Python 3.11, Shard 2/4)	4m 45s
Core Tests (Python 3.11, Shard 1/4)	3m 1s
Core Tests (Python 3.10, Shard 2/4)	5m 29s
Core Tests (Python 3.12, Shard 1/4)	3m 2s
Core Tests (Python 3.12, Shard 3/4)	1m 53s
Core Tests (Python 3.11, Shard 4/4)	2m 40s
	40m 24s