@QuantumGuy You can let JabRef automatically organize your files.
Under Preferences -> Import you can define the Linked file name conenventions.
If you enter [groups:(unknown)] as a file directory pattern JabRef will put the linked files into a folder named after the group(s). If an entry is part of multiple groups, the group folder name is a comma separated list of group names.
If you then use the cleanup operations “Move files to file directory” JabRef will move the linked files to the group.
Newly downloaded paper will then be automatically moved into that directory,.