submodule: remove unnecessary `prefix` based option logic

submodule: remove unnecessary `prefix` based option logic

Over time when parts of submodule have been ported from shell to
builtin, many instances of the submodule helper have been added.
Also added with them are some unnecessary option passing
logic that are based on the `prefix` shell variable which never
gets set in their code flows.

On analysis, the only shell functions which have a valid usage
for the `prefix` shell variable are:

    - cmd_update: which is the only function which sets the variable
      and thus uses it properly

    - cmd_init: which uses the variable via a call from cmd_update

So, remove the unnecessary option parsing logic based on the `prefix`
shell variable.

Signed-off-by: Kaartic Sivaraam <kaartic.sivaraam@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>