That is not a good idea, as you are now violating the architecture: https://github.com/JabRef/jabref/wiki/High-Level-Documentation
You are having gui components in a logic method. This FileUtil method is used in many places.
So I suggest you create a method which throws the exception

I think we need to help @derebaba here a bit (since architectural questions are probably not a good start into a project).

It is also not possible to simply move the dialog service stuff to RenamePdfCleanup since this class also resides in logic. Thus I would propose the following:

1. Extract the body of the FileUtil.renameFile method to a new method FileUtil.renameFileWithException
   

   jabref/src/main/java/org/jabref/logic/util/io/FileUtil.java

   Lines 194 to 199 in c47d2a4

   	if (replaceExisting) {
   	return Files.move(fromFile, fromFile.resolveSibling(toFile),
   	StandardCopyOption.REPLACE_EXISTING) != null;
   	} else {
   	return Files.move(fromFile, fromFile.resolveSibling(toFile)) != null;
   	}

2. Similarly, extract the body of the cleanup method to a new method cleanupWithException (which then uses the new renameFileWithException method)

   jabref/src/main/java/org/jabref/logic/cleanup/RenamePdfCleanup.java

   Line 61 in 8a420b4

   public List<FieldChange> cleanup(BibEntry entry) {

3. Catch the exception and show the error dialog in the gui:
   

   jabref/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

   Line 206 in c47d2a4

   FileUtil.renameFile(fileConflictCheck.get(), file.get(), true);

It's a bit complicated but the best I can come up with (especially since the FileUtil and CleanupJob classes are designed to hide exceptions instead of to expose them). @JabRef/developers what do you think?

Thanks for the comprehensive explanation. I got a little confused at first. Check out my latest commit. It should do the trick if I understand correctly.

Thanks for the quick implementation! The code is exactly how I meant it, good job!
The only problem left is the code duplication from the old methods and the new ones that throw an exception. But this should be easy to fix by calling the withException method in the original one; along the following lines:

public static boolean renameFile(Path fromFile, Path toFile, boolean replaceExisting) {
        try {
            return renameFileWithException(fromFile, toFile, replaceExisting);
        } catch (IOException e) {
            LOGGER.error("Renaming Files failed", e);
            return false;
        }
}

Similarly for the cleanup method. If this is changed as well, I give my 👍 for merge.

I removed the duplicate code as you explained. It is my first contribution ever to an open source project. Thank you for being so helpful.