submodule update: run custom update script for initial populating as well

In 1b4735d9f3 (submodule: no [--merge|--rebase] when newly cloned,
2011-02-17), all actions were defaulted to checkout for populating
a submodule initially, because merging or rebasing makes no sense
in that situation.

Other commands however do make sense, such as the custom command
that was added later (6cb5728c43, submodule update: allow custom
command to update submodule working tree, 2013-07-03).

I am unsure about the "none" command, as I can see an initial
checkout there as a useful thing. On the other hand going strictly
by our own documentation, we should do nothing in case of "none"
as well, because the user asked for it.

Reported-by: Han-Wen Nienhuys <hanwen@google.com>
Signed-off-by: Stefan Beller <sbeller@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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