Addon.d bash script for removing apks after nightly reflash on Android 5.1 CM12.1 not working
This is all made with trial and error and some script copying, I have only vague knowledge of bash and absolutely no idea what I'm risking. All is done with backups and careful reflashes.
#!/sbin/sh
# 
# /system/addon.d/77-MyApps.sh
#
# During a dirty flash, this script will backup files and apps at /system/*
# /system is formatted and reinstalled, then the files are restored.
#

. /tmp/backuptool.functions

list_files() {
cat &lt;&lt;EOF
app/ActionLauncher/base.apk
app/Dropbox/lib/arm/libblasV8.so
app/Dropbox/lib/arm/libDummyArchIndicator.so
app/Dropbox/lib/arm/librsjni.so
app/Dropbox/lib/arm/libRSSupport.so
app/Dropbox/base.apk
app/Eventbrite/base.apk
app/Flud/lib/arm/libclient.so
app/Flud/base.apk
app/GCalendar/base.apk
app/GMail/base.apk
app/GoogleCamera/lib/arm/libgcam.so
app/GoogleCamera/lib/arm/libgcam_swig_jni.so
app/GoogleCamera/lib/arm/libjni_pegutil.so
app/GoogleCamera/lib/arm/libjni_tinyplanet.so
app/GoogleCamera/lib/arm/libjpeg.so
app/GoogleCamera/lib/arm/liblightcycle.so
app/GoogleCamera/lib/arm/libnativehelper_compat_libc++.so
app/GoogleCamera/lib/arm/librefocus.so
app/GoogleCamera/lib/arm/librs.layered_filter_fast_f32.so
app/GoogleCamera/lib/arm/librsjni.so
app/GoogleCamera/lib/arm/libRSSupport.so
app/GoogleCamera/base.apk
app/GPlus/lib/arm/libcrashreporter.so
app/GPlus/lib/arm/libcronet.so
app/GPlus/lib/arm/libframesequence.so
app/GPlus/lib/arm/libphotoeditor_native.so
app/GPlus/lib/arm/libwebp_android.so
app/GPlus/base.apk
app/GPSStatus/base.apk
app/Greenify/base.apk
app/HereMaps/lib/arm/libCertResourcesPkg.so
app/HereMaps/lib/arm/libcrypto_here.so
app/HereMaps/lib/arm/libdatabase_sqlcipher.so
app/HereMaps/lib/arm/gnustl_shared.so
app/HereMaps/lib/arm/libLohitIndicFontPkg.so
app/HereMaps/lib/arm/libMapsEngineResourcePkg.so
app/HereMaps/lib/arm/libMAPSJNI.so
app/HereMaps/lib/arm/libNanumGothicFontPkg.so
app/HereMaps/lib/arm/libNuanceVocalizer.so
app/HereMaps/lib/arm/libposclient.so
app/HereMaps/lib/arm/libPureArabicFontPkg.so
app/HereMaps/lib/arm/libPureChineseFontPkg.so
app/HereMaps/lib/arm/libPureIndicSouthFontPkg.so
app/HereMaps/lib/arm/libPureThaiFontPkg.so
app/HereMaps/lib/arm/libSdkResourcePkg.so
app/HereMaps/lib/arm/libsqlcipher_android.so
app/HereMaps/lib/arm/libssl_here.so
app/HereMaps/lib/arm/libstlport_shared.so
app/HereMaps/base.apk
app/Keep/lib/arm/libsketchology_native.so
app/Keep/base.apk
app/KernelAdiutor/base.apk
app/Orbot/lib/arm/libtun2socks.so
app/Orbot/base.apk
app/Photos/lib/arm/libcrashreporterer.so
app/Photos/lib/arm/libfilterframework_jni.so
app/Photos/lib/arm/libcronet.so
app/Photos/lib/arm/libnative.so
app/Photos/lib/arm/framesequence.so
app/Photos/lib/arm/moviemaker-jni.so
app/Photos/base.apk
app/PlayGames/lib/arm/libgames_rtmp_jni.so
app/PlayGames/base.apk
app/PlayMusic/base.apk
app/Shuttle/base.apk
app/Polycon/base.apk
app/SEftp/base.apk
app/SolidExplorer/lib/arm/lib7z.so
app/SolidExplorer/lib/arm/libgif.so
app/SolidExplorer/base.apk
app/Webview/lib/arm/libwebviewchromium.so
app/Webview/base.apk
app/XDALabs/lib/arm/librealm-jni.so
app/XDALabs/base.apk
app/Xposed/base.apk
app/Youtube/lib/arm/libambisonic_audio_renderer.so
app/Youtube/lib/arm/libcronet.so
app/Youtube/lib/arm/libfilterframework_jni.so
app/Youtube/lib/arm/libluajit.so
app/Youtube/lib/arm/libm2ts_player.so
app/Youtube/lib/arm/libmoxie.so
app/Youtube/lib/arm/libmoxieclient.so
app/Youtube/lib/arm/librsjni.so
app/Youtube/lib/arm/libRSSupport.so
app/Youtube/lib/arm/libvpx.so
app/Youtube/lib/arm/libvpxJNI.so
app/Youtube/lib/arm/libvrtoolkit.so
app/Youtube/lib/arm/libwebp_android.so
app/Youtube/base.apk
EOF
}

case &quot;$1&quot; in
  backup)
    list_files | while read FILE DUMMY; do
      backup_file $S/$FILE
    done
  ;;
  restore)
    list_files | while read FILE REPLACEMENT; do
      R=&quot;&quot;
      [ -n &quot;$REPLACEMENT&quot; ] &amp;&amp; R=&quot;$S/$REPLACEMENT&quot;
      [ -f &quot;$C/$S/$FILE&quot; ] &amp;&amp; restore_file $S/$FILE $R
    done
rm -rf /system/app/Chromium
rm -rf /system/app/Email
rm -rf /system/app/Calendar
rm -rf /system/app/webview
  ;;
  pre-backup)
    # Stub
  ;;
  post-backup)
    # Stub
  ;;
  pre-restore)
    # Stub
  ;;
  post-restore)
    # Stub
  ;;
esac

I have cobbled up this script to back up mine (after plenty of reflashing and restoring) and remove some AOSP alternatives. It seems you must write the code that is to be run after flashing over there (webview is from older AOSP, while Webview is a more streamlined mess). The template is taken from XDA with respect to grinder777. If this works, give yourself a bar of chocolate and send him (her?) a thank. If it doesn't, I have no idea what will, besides what @Android Dev said, but that's not permanent.
EDIT: As YouKnowNothingJohn said, you need at least one backup command. That command could be anything, even a dummy file (at least in &gt;4.4). Thanks Mr. Snow.