Reland: JNI lib is always embedded for APKs in APEX

If a JNI lib is depended on by an APK that is included in an APEX, the
lib is embedded inside the APK.

This change also fixes a bug that APKs are not mutated for APEXes.

Bug: 144135069
Test: m (apex_test.go amended)
Change-Id: I21ac24412b30c05afc03385655c6b196130dffe3