Auto file finder follows symbolic links

CHANGELOG.md

@@ -56,6 +56,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed various issues (including [#5263](https://github.com/JabRef/jabref/issues/5263)) related to copying entries to the clipboard
 - We fixed some display errors in the preferences dialog and replaced some of the controls [#5033](https://github.com/JabRef/jabref/pull/5033) [#5047](https://github.com/JabRef/jabref/pull/5047) [#5062](https://github.com/JabRef/jabref/pull/5062) [#5141](https://github.com/JabRef/jabref/pull/5141) [#5185](https://github.com/JabRef/jabref/pull/5185) [#5265](https://github.com/JabRef/jabref/pull/5265) [#5315](https://github.com/JabRef/jabref/pull/5315) [#5360](https://github.com/JabRef/jabref/pull/5360)
 - We fixed an exception which occurred when trying to import entries without an open library. [#5447](https://github.com/JabRef/jabref/issues/5447)
+- The "Automatically set file links" feature now follows symbolic links. [#5664](https://github.com/JabRef/jabref/issues/5664)
 - After successful import of one or multiple bib entries the main table scrolls to the first imported entry [#5383](https://github.com/JabRef/jabref/issues/5383)
 - We fixed an exception which occurred when an invalid jstyle was loaded. [#5452](https://github.com/JabRef/jabref/issues/5452)
 - We fixed an error where the preview theme did not adapt to the "Dark" mode [#5463](https://github.com/JabRef/jabref/issues/5463)

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

@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.io.UncheckedIOException;
+import java.nio.file.FileVisitOption;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.attribute.BasicFileAttributes;
@@ -87,7 +88,7 @@ private Set<Path> findFilesByExtension(List<Path> directories, List<String> exte
  Set<Path> result = new HashSet<>();
  for (Path directory : directories) {
  if (Files.exists(directory)) {
- try (Stream<Path> pathStream = Files.find(directory, Integer.MAX_VALUE, isFileWithCorrectExtension)) {
+ try (Stream<Path> pathStream = Files.find(directory, Integer.MAX_VALUE, isFileWithCorrectExtension, FileVisitOption.FOLLOW_LINKS)) {
  result.addAll(pathStream.collect(Collectors.toSet()));
  } catch (UncheckedIOException e) {
  throw new IOException("Problem in finding files", e);

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

@@ -3,6 +3,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.UncheckedIOException;
+import java.nio.file.FileVisitOption;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -201,7 +202,7 @@ private List<Path> findFile(final BibEntry entry, final Path directory, final St
  }
 
  private List<Path> collectFilesWithMatcher(Path actualDirectory, BiPredicate<Path, BasicFileAttributes> matcher) {
- try (Stream<Path> pathStream = Files.find(actualDirectory, 1, matcher)) {
+ try (Stream<Path> pathStream = Files.find(actualDirectory, 1, matcher, FileVisitOption.FOLLOW_LINKS)) {
  return pathStream.collect(Collectors.toList());
  } catch (UncheckedIOException | IOException ioe) {
  return Collections.emptyList();