Combine the two separate applications into one
At the moment, gnome-break-timer has two separate executables, with two separate Application classes. This saves a bit of memory in the gnome-break-timer-daemon executable, but it leads to lots of code duplication (BreakManager), and stuff that would otherwise not be needed (the dbus break interface). It also greatly complicates our lives when interacting with Flatpak, and increases the effort to implement new features like usage history.
Instead, let's refactor this thing to use a single GtkApplication and a single main function, where an additional command line parameter is required to open the Break Settings window.