submodule.c: uninitialized submodules are ignored in recursive commands

This was an oversight when working on the working tree modifying commands
recursing into submodules.

To test for uninitialized submodules, introduce another submodule
"uninitialized_sub". Adding it via `submodule add` will activate the
submodule in the preparation area (in create_lib_submodule_repo we
setup all the things in submodule_update_repo), but the later tests
will use a new testing repo that clones the preparation repo
in which the new submodule is not initialized.

By adding it to the branch "add_sub1", which is the starting point of
all other branches, we have wide coverage.

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

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