submodule.c: fetch in submodules git directory instead of in worktree

Keep the properties introduced in 10f5c52656 (submodule: avoid
auto-discovery in prepare_submodule_repo_env(), 2016-09-01), by fixating
the git directory of the submodule.

Signed-off-by: Stefan Beller <sbeller@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>