setup: allow for prefix to be passed to git commands

setup: allow for prefix to be passed to git commands

In a future patch child processes which act on submodules need a little
more context about the original command that was invoked.  This patch
teaches git to use the prefix stored in `GIT_INTERNAL_TOPLEVEL_PREFIX`
instead of the prefix that was potentally found during the git directory
setup process.

Signed-off-by: Brandon Williams <bmwill@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>