test: do not use .keep in objects/ and refs/ git administrative folders

This .keep empty file was here because git does not keep empty directories, but the expected status for the test was to have empty directories. After updating from git 2.48.0 to 2.52.0 this started to cause test failures with:

error: refs/.keep: badRefName: invalid refname format

Instead of using marker files, do not store these empty directories in git and create them during the test setup.