setup: stop using `the_repository` in `set_git_work_tree()`

setup: stop using `the_repository` in `set_git_work_tree()`

Stop using `the_repository` in `set_git_work_tree()` and instead accept
the repository as a parameter. The injection of `the_repository` is thus
bumped one level higher, where callers now pass it in explicitly.

Similar as with the preceding commit, we track whether the worktree has
been initialized already via a global variable so that we can die in
case the repository is re-initialized with a different worktree path.
Store this info in the `struct repository` instead so that we correctly
handle this per repository.

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