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I know that the backup includes the rc.local file with the  startup script and that works fine but it's not enough for my usecase. I use the user startup script to start 2 custom shell scripts but the scripts aren't included in the backup so the backup isn't useful.

Is there a way to get my custom scripts included in the backup? currently they are sitting in the /etc/ folder but the backup isn't working.

I know that I could just use scp or something like that but it would be nice if people who aren't that tech savvy could just use the webui to upload a backup file to the router.

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I figured it out myself. I can add the custom scripts to the backup archive I downloaded manually and when I upload that backup to the router it will also upload the scripts.
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You can add the absolute file location of your script in file
/etc/sysupgrade.conf

After that your file will be included in the backup archive. Furthermore the file will be remained after firmware upgrade.