gitlab-shell uses completely own whole set of git hooks and just
symlinks repo.git/hooks to path/to/gitlab-shell/hooks/.

Original hooks that git added there - when initializing repository -
from its template, and which are by default deactivated, are currently
moved to repos.git/hooks.old.<timestamp>, e.g.

$ ls -F nexedi/helloweb.git/
    config
    description
    HEAD
    hooks@                  -->  ...path/to/gitlab-shell/hooks/
    hooks.old.1446564288/
    info/
    packed-refs
    refs/

$ ls -F nexedi/helloweb.git/hooks.old.1446564288/
    applypatch-msg.sample*
    post-update.sample*
    pre-commit.sample*
    pre-push.sample*
    update.sample*
    commit-msg.sample*
    pre-applypatch.sample*
    prepare-commit-msg.sample*
    pre-rebase.sample*

On the other hand, hooks.old.<timestamp> are not used anywhere and are
left there "just in case". But what is the point to keep those pristine
samples git creates by default? And we are sure those files are always
results of gitlab-shell initializing a repository, as it is
gitlab-shell's job to create/remove/update/etc repositories.

So do not keep old hooks, remove them.

P.S. The patch that introduced whole-hooks-dir-symlinking is
    db81327b (Symlink the whole hooks directory).

/cc @dzaporozhets, @jacobvosmaer