Have Fluxer run in the Background

Forgive me if I am wrong; but, do you mean you want the same type of behavior as #918? Where you Minimize/Close the application to the tray so you can still get notifications and messages rather than actually having the application completely end its task? I don't know what linux distro you use; but, all of the ones I have used have had system trays for managing tasks that are somewhere between foreground and background.