On a M$ system, I agree with using the config file in the installdir as the first choice. But, on a Linux/Unix system, the concept of searching the user's home first goes way back. For me, that is over 35 years. If the program is started by root, or at startup, then a home config file won't necessarily be found/created. Then a /etc location would be searched next. In this case usually a place like /etc/nzbget/nzbget.conf. Lastly the installdir location.
So, what happens if something is changed in the config file?
Well, it isn't a launch script specifically. It is an alias. The nzbget program isn't in my path, so I need a way to point to it anyway. Having an alias is a quick and dirty way to do it. But, I'll keep the symlink idea in mind.I think I have an (alternative) solution for you: instead of creating a launch script you can symlink the config-file from home dir into installation dir. That prevents creating of new config file on update.
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