clone: do not let --depth imply --shallow-submodules

In v2.9.0, we prematurely flipped the default to force cloning
submodules shallowly, when the superproject is getting cloned
shallowly.  This is likely to fail when the upstream repositories
submodules are cloned from a repository that is not prepared to
serve histories that ends at a commit that is not at the tip of a
branch, and we know the world is not yet ready.

Use a safer default to clone the submodules fully, unless the user
tells us that she knows that the upstream repository of the
submodules are willing to cooperate with "--shallow-submodules"
option.

Noticed-by: Vadim Eisenberg <VADIME@il.ibm.com>
Helped-by: Jeff King <peff@peff.net>
Helped-by: Stefan Beller <sbeller@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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