Hello! It will be very nice to add ability for search installed flatpak applications in whisker menu (like gnome-shell do). "Flatpak expects window managers to respect the XDG_DATA_DIRS environment variable to discover applications.": https://wiki.archlinux.org/index.php/Flatpak#Adding_Flatpak_.desktop_files_to_your_menu
I installed the Gimp application from flatpak and it appears in my menu (in both application menu and whisker menu), in Graphics section. Note that you need to reload your desktop to allow your system to read /etc/profile.d/flatpak.sh which add "$HOME/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share" to your $XDG_DATA_DIRS paths. Also, https://github.com/flatpak/flatpak/issues/1286#issuecomment-354554684 explain how the .desktop files works with flatpak.
Thank you for reply. In Fedora 28 all works as expected, Have a nice day.