Sync model and helper files from master branch

This patch backports everything related to FlatpakReference class, which
we need to get in sync in order to be able to cherry-pick multi-level
overrides soon.

cherry picked from the following commits:
43d1ebf1
6363d6fc
27357a84
18bde3dc
f7ea88c5
7b79a6d0
204dfa3c
10edd2c4
4c246ce4
a4ab810d
e567bd02