A Package can currently only be created efficiently if all of the files you want are in one folder together, and nothing else that you don't want in the Package is in that folder. If this were always the case, there would be less of a need to create a Package since all of the information could already be easily found in a folder. To create a package where the files you want are part of a large folder and buried among many other files you do not want, there is no way to search except by filename or title.
Please consider adding search parameters here so that files can be added in bulk. E.g., ability to search for all files of a certain revision, or all files belonging to a specific submission, etc.