When a repository is cloned by using simple
git clone repo
git clone --no-checkout doesn't give a bare repository, it just leaves the work tree and index empty.
git status after such a clone will say that all files have been staged for deletion.
A bare repository is one with
core.bare = true (and a bare repository made with
git clone --bare will also not have any remote refs). You can do
git config core.bare true to flip this bit. Then remove the work tree and index, and possibly rename the directory from