Fix and improve reference cache mod-union table

Improvements:
Remove cards that only contain null references, this can save memory
in some cases.

Fixes:
Fix a bug where the mod-union table didn't properly handle class
loaders in the boot image. This was cause by not adding the new
classes as references. The fix is to leave these cards dirty.

Bug: 23203999
Change-Id: Ib1f1f74154df976dd8abaf2430c6dabd4cae2dbe