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The file sysupgrade.conf contains files and dirs preserved during an firmware upgrade: whatever the option "keep all settings" or not ?

As the /etc/rc.d directory is inside, the user scripts should be stored in /etc/rc.d and the calls in /etc/rc.local: correct ?

Why the /etc/rc.local file is not in sysupgrade.conf ?

What is the difference if I store my scripts in /etc/config ?

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Sysupgrade.conf preserves files and directories when "keep all settings" is selected, when this flag isn't selected, device gets reset to default settings.
Sysupgrade.conf also preserves files into backup configuration which can be downloaded in WebUI -> System -> Administration -> Backup, so all scripts, directories and configuration files can be transferred to devices with identical hardware.

Standard practice is to store user scripts into /usr/sbin directory and if you want to preserve them, include path to it into sysupgrade.conf file.