The issue is here:

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

Line 451 in a080191

    
           String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileDirPattern());

If the parameter is empty string the citeky is returned.

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

Lines 283 to 288 in 7cc5747

    
           public static String createDirNameFromPattern(BibDatabase database, BibEntry entry, String directoryNamePattern) { 
        
               String targetName = BracketedPattern.expandBrackets(directoryNamePattern, ';', entry, database); 
        
               if (targetName.isEmpty()) { 
        
                   targetName = entry.getCiteKeyOptional().orElse("default"); 
        
               }

	public static String createDirNameFromPattern(BibDatabase database, BibEntry entry, String directoryNamePattern) {
	String targetName = BracketedPattern.expandBrackets(directoryNamePattern, ';', entry, database);

	if (targetName.isEmpty()) {
	targetName = entry.getCiteKeyOptional().orElse("default");
	}

Uh oh!

Download of files put them in subfolders #6589

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