Create a New Mimetype
We have to teach the system about GuitarPro as something called a "mimetype". To do that, we need to create a mimetype package file that contains info about how to identify GuitarPro files.
Create a new file called "guitarpro.xml" at "/usr/share/mime/packages"
In this file we need to make some rules about how to match files to this ...
Maybe Code is overriding Files' association to open folders (inode/directory)?
Yes, that is the case. Both have an association with inode/directory in their .desktop file. Somehow Code's association gets priority (my guess is either it goes to the most recently updated application or the one with the name in the earliest alphanumerical order).
This can be ...
Compare the .desktop file of mtpaint with another .desktop file of an app that works and see what's missing or what's different.
You might need to add %U at the line Exec, so you will have: Exec=mtpaint %U