In some cases, we need delete META-INF dir to void mis-using some
classes files in the Java runtime.
For now, when we delete META-INF, we need keep Manifest file in the jar
since merge_zips doesn't have ability to add a default one.
Bug: b/65455145
Test: m clean && m -j
Change-Id: Iea44b1a98d348cd8df1fa7374907733b1add6935
Also filter out META-INF/TRANSITIVE dir, and report warnings when
merge_zips see duplicates entries with different CRC hash.
Bug: b/65455145
Test: m clean && m -j java (locally)
Change-Id: I47172ffa27df71f3280f35f6b540a7b5a0c14550
