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gs-application.c: Show update preferences if flatpak enabled (LP: #1791553)

@robert.ancell This is a version of !5 (merged) for the 3-30 branch.

Note I did the check after gs_application_initialize_ui as that is where the plugins are init'd (as this method then calls gs_application_initialize_plugins).

I have tested this on a cosmic machine with/without the flatpak plugin loaded and it acts as I would expect.

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