It seems upstream wants that you can save multiple configurations. 
What do you think about this idea (based in yours)?:

1.- If you save the settings, the default file would be

2.- If ~/.gpsprune/.pruneconfig exists, it would be the default

3.- If ~/.gpsprune/.pruneconfig doesn't exist, gpsprune would find
a .pruneconfig file in the current folder (as it is doing now).

4.- Altough the default file to save configuration files would be
~/.gpsprune/.pruneconfig, you have the choice to save the settings file
in another place with another name.

5.- If you don't want the default settings, you can load another
configuration if you want, through a new "Load settings" item in
"Settings menu".

If you like this idea, I can forward it to upstream.
If you don't like, please tell me if it can be improved.

Thanks for your collaboration!

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