Ignore submodule on checkout instead of deleting it

Ignore submodule on checkout instead of deleting it

The purpose of this commit is to prevent destruction of
submodules on checkout from a tree with a submodule to
another. For consistency we handle the reverse case too,
when we checkout a branch that has a submodule and the
submodule directory exists. And finally we ignore the
case where the submodule changes.

We do not update the submodules, we just try to ignore
them harder.

Bug: 356664
Change-Id: I202c695a57af99b13d0d7220803fd08def3d9b5e
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>