To run the user’s configured application you can plug the desktop interface and then call xdg-open from within the snap.
Unfortunately however there is no way to run external applications like say gnome-terminal from the host machine due to the strict confinement sandbox. Whilst there is now the desktop-launch interface to launch other applications from a snap, it is designed for a fully snapped desktop environment (imagine gnome-shell as a snap) so I am not sure it is appropriate in this case.
However, I expect most users would expect a file manager to be able to access any file which they have access to on the host, and to run in the same mount namespace etc - similar to say an IDE or terminal emulator, both of which already have exceptions for classic confinement. As such, @pedronis or @niemeyer could you please weigh in to clarify whether perhaps we could create a new category for classic confinement for snaps that are traditional file managers? Thanks.