Don't create or modify flatpak manifests
The integration of the build configuration with Flatpaks seems modifies the manifest file, even when the user didn't change anything either in the build configuration or in the manifest. Builder should avoid these, since the manifest is usually necessary to be edited by hand.
Also, when changing branches with git checkout
the old build configurations are preserved, and because of the previous point, it creates spurious manifest files in the repo, picking the wrong one.