META-INF/INDEX.LIST files are pointless in an executable jar and
moving application classes from the root of the jar to
BOOT-INF/classes breaks the index, resulting in an
InvalidJarIndexException being thrown.
This commit updates the Repackager to automatically remove a
META-INF/INDEX.LIST file from a jar file that is being repackaged.
Closes gh-6601
899b851c6f