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By now steps to use flatpak are:

use steps in #34 (closed) to make room for flatpak runtime and apps. At some point it will be done automatically with cloud-initramfs-growroot. See image-builder!39 (merged)

sudo flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

As an example install and configure Fractal:

sudo flatpak install flathub org.gnome.Fractal

Although there's a XDG_DATA_DIRS for purism user, it is not accesible for phosh, so it cannot read the desktop application installed by flatpak. You can check environment for phosh with:

xargs -n 1 -0 < /proc/$(ps -ef | grep phos[h] | grep -v rootston | awk '{print $2}')/environ

So we override that with:

sudo systemctl edit phosh.service

with this contents:

[Service]
Environment=XDG_DATA_DIRS=/home/purism/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share

Then add Fractal to favorites with:

gsettings set sm.puri.phosh favorites "['org.gnome.Contacts.desktop', 'org.gnome.Epiphany.desktop', 'org.gnome.Terminal.desktop', 'org.gnome.Fractal.desktop']"