builtin/clone: fix leaking repo state when cloning with bundle URIs

builtin/clone: fix leaking repo state when cloning with bundle URIs

When cloning with bundle URIs we re-initialize `the_repository` after
having fetched the bundle. This causes a bunch of memory leaks though
because we do not release its previous state.

These leaks can be plugged by calling `repo_clear()` before we call
`repo_init()`. But this causes another issue because the remote that we
used is tied to the lifetime of the repository's remote state, which
would also get released. We thus have to make sure that it does not get
free'd under our feet.

Signed-off-by: Patrick Steinhardt <ps@pks.im>
Signed-off-by: Junio C Hamano <gitster@pobox.com>