flatpak: Reorder modules in the manifest
Our manifest has kept its structure right from when it was just a prototype, and given the number of dependencies Boxes has, it has become quite messy.
These changes benefit from flatpak-builder's capability of using nested modules[0], which allows for a clearer order for modules and their leaf dependencies.
This also drops the space before the colon in JSON, because that's just silly. :)
https://docs.flatpak.org/en/latest/flatpak-builder-command-reference.html