Use add_sourceapp.sh from the Open GApps project root, when updating files in app, priv-app, lib or lib64.
The other directories are to be maintained manually. Permissions must be sorted alphabetically.

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Some APKs can only be retrieved from nexus images:
Download one of the latest Nexus Phone images from https://developers.google.com/android/nexus/image
If you don't use the image of a phone, some applications and libraries might miss, like the camera and/or the dialer.
Pay also attention that APK files are not lacking their classes.dex!

Extract the image-xxxxx-xxxxxx.zip from from the tgz archive
Extract the system.img from the image-xxxxx-xxxxxx.zip
Get sig2img from https://github.com/anestisb/android-simg2img
Convert the system.img from a sparse android file to a disk-image file using android-simg2img: simg2img system.img system.raw.img
Open the system.raw.img using a disk-mount application

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Import the following apks from the Nexus image using the add_sourceapp.sh:
/app/GoogleContactsSyncAdapter/GoogleContactsSyncAdapter.apk
/priv-app/GoogleBackupTransport/GoogleBackupTransport.apk
/priv-app/GoogleFeedback/GoogleFeedback.apk
/priv-app/GoogleLoginService/GoogleLoginService.apk
/priv-app/GoogleOneTimeInitializer/GoogleOneTimeInitializer.apk
/priv-app/GooglePartnerSetup/GooglePartnerSetup.apk
/priv-app/GoogleServicesFramework/GoogleServicesFramework.apk
/priv-app/SetupWizard/SetupWizard.apk
/priv-app/TagGoogle/TagGoogle.apk
/lib/libjni_latinimegoogle.so

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Copy the following files and folders from the Nexus system image to their corresponding folder.
Note that only the lib*.so files are architecture dependent, the other files can go into 'all':
/etc/permissions/com.google.android.camera2.xml
/etc/permissions/com.google.android.dialer.support.xml
/etc/permissions/com.google.android.maps.xml
/etc/permissions/com.google.android.media.effects.xml
/etc/permissions/com.google.widevine.software.drm.xml
/etc/preferred-apps/google.xml
/framework/com.google.android.camera2.jar
/framework/com.google.android.maps.jar
/framework/com.google.android.media.effects.jar
/framework/com.google.widevine.software.drm.jar
/usr/srec
/vendor/pittpatt