system-helper: Centralize pid-setting
system-helper: Centralize pid-setting

There was a bunch of handle methods which forgot to do
this manually, so call the flatpak_dir_set_source_pid()
method right when we create the FlatpakDir object.

Closes: #2384
Approved by: alexlarsson

flatpak/flatpak,flatpak/flatpak,matthiasclasen/flatpak,flatpak/flatpak,matthiasclasen/flatpak,matthiasclasen/flatpak,flatpak/flatpak,flatpak/flatpak,matthiasclasen/flatpak,matthiasclasen/flatpak