We shrink the source and destination arrays, but not the modes or
submodule_gitfile arrays, resulting in potentially mismatched data. Shrink
all the arrays at the same time to prevent this. Add tests to ensure the
problem does not recur.
Signed-off-by: brian m. carlson <sandals@crustytoothpaste.net> Signed-off-by: Junio C Hamano <gitster@pobox.com>