I have always stored all my .bib files in a single directory with the linked files stored in another directory. In the library properties I have set the the “general file directory” as a relative path …/…/Papers.
The reason I specify the file directory as a relative path is that I use the jabref library on multiple computers, the jabref file and linked documents are stored in my onedrive. If I set an absolute path for the file directory I need to update it on each computer as the usernames are not the same. This has worked well for years now.
In 5.1 and earlier my workflow was link files using the entry editor then right click and select move to file directory. If I was adding multiple files I would select multiple entries and use the clean up entries (Alt + F8) & move files to default file directory. Either method would copy files to my “Papers” folder.
In 5.2 there was a small bug where the right click menu item disappeared. This was not to much of a problem as I could use the clean up entries method I describe above. However, even though I still have the default file directory set (all my linked documents open correctly) new files are moved to the location of my Jabref file.
I have now installed version 5.3 ( main - builds.jabref.org > main). This fixes the right click move file to file directory option. However, files are still moved to the folder location of my bibtex file and not the file directory I specified (Papers).
My workaround it to let a couple of documents build up in my jabref file directory before manually copying them across to my default file directory. This is not a big issue but was wondering if a proper fix/workaround is available.