sh-fix-rugged-tree-entries.yml

The Rugged implementation was recursively scanning the repository to
create `flat_path` because the post-process step was being called from
with a loop. For large repositories, this was significantly slowing
things down. Break the call to `rugged_populate_flat_path` out of this
loop to make this work efficiently.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/59759