I want to have different Flatpaks completely pre-installed in my image. My current problem is that the Flatpaks seem to only start installing 1-2 minutes AFTER I boot to the OS for the first time, which is very annoying. How can I have a flatpak like Bazaar come pre-baked in my image?

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That's not possible. You can only preload it into the ISO.

HeliumOS actually used to do this, you can install flatpaks to a custom directory somehow, and they will be immutably part of the custom image