First the disclaimer:

The Geany developers strongly discourage running Geany (or any IDE) as 
superuser.  An IDE by its very nature makes it easy to execute arbitrary 
commands, programs, and worst of all programs __users__ wrote.  The files that 
need to be edited by superuser are simple and do not need a whole IDE, its best 
to use a simple editor of your choice.  Any damage or difficulties related to 
running Geany as superuser are not the responsibility of the Geany developers.

Then the answer:

One of the things sudo can do is change the working directory to the new user, 
so Geany run as another user is not accessing the config in the user directory 
any more.

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