Add new functionality for the Flatpak runtime

This adds several features I'm using for the Flatpak runtime:

• extend: manifest.yaml, to have one runtime extend another (used for the graphical one to extend the headless one).
• SDK-specific pre_apt_script, to avoid enabling the development repository on the non-SDK runtime.
• --override-packages, to use local versions of packages for testing (used to test the flatpak-xdg-utils package).