Update flatpak manifest

I removed unneeded permissions for the filesystem home folder and dbus. I added rename-icon to fix the application icon, and commit in the dependency source to ensure reproducibility.

I seem to not be able to run the flatpak however, I get "Couldn't register name 'org.kde.Keysmith' with DBUS - another process owns it already!" for some reason. This is also the case on master though.