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tests: missing refs/ in bare repositories (#28844) (#28852)

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Backport #28844 by @AdamMajer

Git 2.43.0 will not detect a git repository as valid without refs/
subdirectory present. `git gc` cleans this up and puts it in
packed-refs. We must keep refs/ non-empty.

Co-authored-by: Adam Majer <amajer@suse.de>
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