I’m not familiar with jabref, so I probably shouldn’t stick my oar in here. But I will anyway. I’ve written my own python script that I use for lists like Web bookmarks. It’s a poor man’s database manager, so you can add attributes to bookmark entries and sort and search on those attributes.
<plugging package=“file_manager”>FileZilla</plugging>
-or-
<plugging package=“file_manager”>Gnome Commander</plugging>
…but call me quaint. I still like…
<plugging package=“file_manager”>mc</plugging>
… 'cause it always just works. mc can ostensibly preserve attributes, time-stamps, and (with appropriate privilege on the receiving end) ownership of transferred files (using an sftp server supposedly).