Instead of giving up on directory subtraction entirely, try to
subtract directories that are in an included manifest *and* do not
have a non-directory file somewhere in their path.
For example:
bundle1:
/dir/file
bundle2: includes bundle1
/dir
In this case /dir would be subtracted from bundle2.
Also add a special case for subtracting directories if they are in
os-core as this reduces a lot of unused content from a bundle's
manifest.
Signed-off-by: William Douglas <william.douglas@intel.com>