Your zero-warning auto renaming of library files destroyed years of work in seconds

On Tue 2023-12-12, I copied my primary bib file, library.bib to my desktop while JabRef was open. I then appended a date to the filename to keep it as a backup and moved the new filename back into my main library fold. JabRef then proceeded, within less than a minute and with no warning or “Do you wish to proceed?” query, to obliterate about a decade’s worth of carefully-done, very-high-value filenames by renaming every one of them to the name of the bib file I had just moved in, replacing each high-value name with the name of the bib file I had just moved into the folder plus a counting integer. Before I could understand what was happening, years of scrupulously careful and extremely useful (readable filenames have high value for articles) work was destroyed.

I did not even swear. All I could do for about half an hour was scream, “WHY?” and try to keep from having a full breakdown. In decades of work in software, I’ve never seen programming so dangerous as destroying years of work in seconds due to the user doing one of the normally safest moves imaginable: moving a file into a folder. The fact that someone had designed this ability as something they thought would be “helpful” made it even worse.

To whoever the new members of your team are that have decided you have total ownership of whatever folder JabRef happens to be running in and can change filenames as you please, let me make this as clear as possible: You do not. Thinking you do is akin to deciding you can design a viper pit into someone’s living room and let them bear the consequences of not first reading whatever you decided made such pits extremely valuable and necessary for everyone.

I assume this is the same group that keeps destroying filenames that I carefully enter into bib texts, replacing them with some combination of downloads I never asked for and never wanted and links that are nothing like what I entered and, incidentally, never work after doing this minor destruction. Also, files I click on no longer appear in the tools automatically; they force me to click a blinking icon.

I want to keep using JabRef, given my investment in it. However, given the mind-bogglingly foolish decisions someone is making lately, I may have to find another tool. The correct design for a tool like this is to accommodate diverse user styles, never embed upward-pointing knives in carpets, and never assume you have more ownership over library files than whoever worked for years to create them, even if you incorrectly think it’s more “efficient.”

On the bright side, my backup service worked, though I was too distraught for at least half an hour to realize that I might still recover all my work.

So again, do not plant incredibly dangerous traps in your software and then pat yourselves on the back over how “efficient” you can be by ignoring and not caring what other folk’s library designs might be. If the person creating these traps cannot stop themselves, then others with more sense to exclude them from the project. If it is a project lead, you need a new project lead. None of this is acceptable software design in any community.


Thanks for reaching out to us, and we are deeply sorry for what happened to you, and we are trying to investigate what led to this action. We are aware of different use cases and user bases in JabRef and try to accommodate the best for each. However, as JabRef normally does only rename files if it’s configured to do so, we would need more details to help reproduce and prevent possible reoccurrence of this problem

  1. Which version of JabRef are you using?
  2. Do you have any save actions enabled (Library properties → Save actions)?
  3. What does your citation pattern look like?
  4. How are your linked files settings defined? Do you have any pattern configured, and what does your folder setup look like? (Main file directory, or a directory configured in the library properties)
  5. Where is your bib file stored? Next to the pdfs in the same folder?

Just to get it right. You had a bib file opened in Folder A where your pdfs are stored. Then you copied to the desktop, renamed it and copied it back to the same folder?

JabRef also keeps backups of library files after saving.

Best regards

What you report is a serious issue and I can assure you something like this is by no means intentional JabRef behaviour.

For context, here is one way how JabRef CAN change filenames in bulk, but only, if manually triggered to do so:

  1. Set a pattern in Linked File name conventions:
  2. Go to Quality > Cleanup Entries (ALT + F8) and choose Rename files to given filename format pattern and click ok.

To my knowledge, there does not seem to be an option in the GUI under library properties → save actions to trigger a linked file rename.

To be honest, I am slightly confused. Could you please clarify, if

a) your .bib files in your main library fold (outside of JabRef) were renamed?
b) your linked files (e.g. pdfs) in your main library fold (outside of JabRef) were renamed?
c) or your linked files data in an entry WITHIN JabRef were renamed?

Also, how did the complete filename look like with the date? “library2023-12-12.bib”? I would like to reproduce, but without exact steps, it is hard to do so.