Thanks bhigham and disciplepup.
For bhigham: Despite the existence of packages.txt and other files in ./root/packages, the problem happened.
For disciplepup: The workaround you gave was what i actually did to install additional files. However, it would be nice if the gpkgtool worked as intended.
Somebody please help!
EDIT: I misread the name of the file. I'll look if pkgsource.txt is there as well.