Refactoring of code to remove it from main and more #542

Job	Run time
Run pipeline with test data (24.04.2 \| docker \| test)	3m 33s
Run pipeline with test data (24.04.2 \| docker \| test_alphafold2_split)	5m 31s
Run pipeline with test data (24.04.2 \| docker \| test_alphafold2_download)	4m 18s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_local)	4m 45s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_webserver)	5m 41s
Run pipeline with test data (24.04.2 \| docker \| test_colabfold_download)	5m 43s
Run pipeline with test data (24.04.2 \| docker \| test_esmfold)	6m 48s
Run pipeline with test data (latest-everything \| docker \| test)	5m 4s
Run pipeline with test data (latest-everything \| docker \| test_alphafold2_split)	5m 40s
Run pipeline with test data (latest-everything \| docker \| test_alphafold2_download)	7m 2s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_local)	5m 12s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_webserver)	3m 29s
Run pipeline with test data (latest-everything \| docker \| test_colabfold_download)	12m 49s
Run pipeline with test data (latest-everything \| docker \| test_esmfold)	5m 11s
	1h 20m 46s

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