File links not updated after "Copy linked files to folder" and cleanup — PDFs still point to original paths

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1

Summary

I imported PDFs from multiple scattered directories into a single .bib library
via JabKit (convert --input-format=pdfMerged). The file fields contain
absolute paths to the original locations (deep nested Zotero-style directories).

I want to consolidate all PDFs into one folder next to the .bib file. I tried
the built-in tools, but the file links in the database are not updated — opening
a PDF from JabRef still tries to access the original path.

Steps to reproduce

  1. Import PDFs from multiple folders into a .bib library using JabKit:
    jabkit convert --input= --input-format=pdfMerged
    –output=library.bib --output-format=bibtex
    The resulting entries have file fields like:
    file = {:/home/user/data/paper/ref/rsa_method/2019_Popal …/origin.pdf:PDF}

  2. Open library.bib in JabRef.

  3. Set the Main file directory in Library Properties → General.

  4. Click Library → Copy linked files to folder. Files are copied to the
    target folder.

  5. Run Quality → Cleanup entries, enable file-related options:

  • “Move to file directory”
  • “Make paths relative”
  • “Rename files to match citation key”
  1. Save the library.

Expected behavior

After step 5, the file field in each entry should be updated to point to the
new location. Opening a PDF from JabRef should use the new path.

Actual behavior

The files are physically copied to the target folder, but the file field in

What I’ve tried

Environment

  • JabRef 5.15–2024-07-10–1eb3493
  • Linux 6.17.0-22-generic amd64
  • Java 21.0.2
  • JavaFX 22.0.1+7

Question

Is there a correct workflow to both copy PDFs to a single folder and update
the file links in the database? Or is this a bug where “Copy linked files to
folder” doesn’t trigger the link update?

2

Thanks for your issue. We will look into this! Have you tried the latest development version from builds.jabref.org ?