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fix: apply preferred_branch after cloning in _clone_repo_from_config #70

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Job	Run time
docs	17s
lint	7s
test (ubuntu-latest, 3.12)	1m 0s
test (macos-latest, 3.13)	45s
test (windows-latest, 3.11)	2m 21s
test (ubuntu-latest, 3.11)	57s
test (macos-latest, 3.11)	49s
test (windows-latest, 3.13)	2m 5s
test (ubuntu-latest, 3.13)	58s
test (macos-latest, 3.12)	47s
test (windows-latest, 3.12)	2m 5s
	12m 11s