> nbeerli@galaxy3:~$ ls -la ~/.config/geany ls: cannot open directory 
> '/home/nbeerli/.config/geany': Permission denied nbeerli@galaxy3:~$

This is your problem.
What does `ls -la ~/.config` give?

Did you tried to start Geany as root (e.g. with `sudo`) before or anything else?

To solve your problem: make sure your user can write to his own configuration 
directory. How to do that depends on the output of the ls command above.

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