Save package dex usage info after secondary dex reconciliation

Bug: 1833991
Test: add a bogus entry to /syste/data/package-dex-usage.list
      adb shell cmd package reconcile-secondary-dex-files
com.android.google.gms
      wait a bit and check the bogus entry is gone

Change-Id: Ic07126bfb8730933081a5e010e3c357d338786e8