lib/oe/patch: handle patches that delete files with older git

lib/oe/patch: handle patches that delete files with older git

When running "git add" on a directory with older git versions, deleted
files aren't added to what is to be committed unless you explicitly
specify the -A option. The result of this is that when applying a patch
from a recipe which doesn't apply with "git am" (and we fall back to
applying the patch through other means then "git add" following by
a "git commit") these deletes weren't committed with the patch, leaving
them sitting deleted but not committed at the end.

This should fix test_devtool_modify_native (which unwittingly exercises
this scenario by attempting to run "devtool modify" on apt-native) on
machines with older git versions.

Signed-off-by: Paul Eggleton <paul.eggleton@linux.intel.com>
Signed-off-by: Ross Burton <ross.burton@intel.com>