Flatpak 1.3.2 is now available and it contains a major change in how installation of Flatpak apps is done system-wide as a user. The developers decided to rewrite the setup process of a Flatpak app due to the fact that the previous method caused unnecessary I/O and used more disk space. The new setup process relies on a custom FUSE file system. But it appears that there's also a downside of the new system-wide installation method, which apparently makes the packaging of a Flatpak app more complex due to it requiring to have a "flatpak" user already added in the package. Packagers can change the default user with the --with-system-helper-user=USERNAME parameter.