Edit the package in the sequencer, next copy the files and folders you want on the local system. So on the sequencer itself, after that you can add them to the package.
So if you want to move a folder in the package, delete the folder from the package, create the folder on the local system at the location you want it to be then re-add it.
This can be a painful and slow process if you have multiple files/folders. It might be better than to update the package or re-sequence.
