Gitlab fsck configuration

I have a self-hosted gitlab instance and gitlab reports that 16 repositories have failed repository checks - all are related to double / in submodule URLs. I can fix this issue (without rewriting history) locally per repository with fsck.skiplist configuration:

Example for one repository:
.gitconfig

[fsck]
	skipList = .git-fsck-skiplist

.git-fsck-skiplist

# Double slahes in submodule url
6f5c32ccaa6e973f6968840919d549c10dda1230

How can I tell gitlab to use such .gitconfig or fsck.skiplist for a particular repository. I understand it is possible to edit global .gitconfig for gitlab but this doesn’t seem a feasible option because we have a lot of repositories and fsck fails if it doesn’t find fsck.skiplist file