Fix dex flags for secondary dex files

getDexFlags should always be called after getRealCompilerFilter.
Otherwise public dex files might be considered private and their oat
file will not be readable by others.

Bug: 36896515
Test: adb shell cmd package compile -r bg-dexopt  --secondary-dex com.google.android.gms
      check that the oat directory and files have the right permissions

Change-Id: Ic91957f155c2008ed59a7e2ba14732e5af88d12a