Repos are overwritten by Pungi during composes in the Fedora infra and
Pungi currently only overwrites the leaf manifest.
See: https://pagure.io/releng/issue/11969
Reverts: 49db8be manifests: Move repos config to common manifest
Use a filtered comps group to add essential apps instead of manually
listing them in the manifest.
Also add gparted to the image as it needs privileges thus it can't run
as a Flatpak.
