Jar always puts default MANIFEST.MF files in if none was specified.
Copying that behavior in soong_zip causes problems with merge_zips,
because it ends up taking the default manifest from the classes.jar
instead of the user's manifest from res.jar. We don't want the
user's manifest in the classes.jar, otherwise a change to the
manifest will cause all the class files to rebuild. Instead,
move the manifest insertion to the final merge_zips stage.
Test: m -j checkbuild
Change-Id: Id6376961dbaf743c2fb92843f9bdf2e44b963be0
