Fix bug in APK entry alignment.

APK entry alignment logic assumes that input entries have zero-length
comment and extra fields. When the assumption is broken, the logic
silently breaks alignment of output entries. This happens, for
example, when the APK to be signed is already aligned and thus may
contain entries with non-empty extra fields.

Given that APKs are not supposed to use comment and extra fields for
anything useful and given that this signer already discards comment
and extra fields of compressed entries, this change makes the signer
discard comment and extra fields of STORED input entries as well.
This unbreaks the existing alignment logic.

Bug: 27814973
Change-Id: I8242b037e21ba7bcf45d0fe2afc8bfc47f1ec314