Fix: Make FileUtil.relativize symlink-aware

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

@@ -256,15 +256,40 @@ public static Path relativize(Path file, List<Path> directories) {
         if (!file.isAbsolute()) {
             return file;
         }
+        Optional<Path> realFileOpt = tryRealPath(file);
 
         for (Path directory : directories) {
+            Optional<Path> realDirOpt = tryRealPath(directory);
+
+            if (realFileOpt.isPresent() && realDirOpt.isPresent()) {
+                Path realFile = realFileOpt.get();
+                Path realDir = realDirOpt.get();
+                if (realFile.startsWith(realDir)) {
+                    int nameCountToDrop = realDir.getNameCount();
+                    Path relativePart = realFile.subpath(nameCountToDrop, realFile.getNameCount());
+                    return relativePart;
+                }
+            }
+
             if (file.startsWith(directory)) {
                 return directory.relativize(file);
             }
         }
         return file;
     }
 
+    private static Optional<Path> tryRealPath(Path path) {
+        if (Files.exists(path)) {
+            try {
+                return Optional.of(path.toRealPath());
+            } catch (IOException e) {
+                return Optional.empty();
+            }
+        } else {
+            return Optional.of(path.toAbsolutePath());
+        }
+    }
+
     /**
      * Converts an absolute file to a relative one, if possible. Returns the parameter file itself if no shortening is
      * possible.

jablib/src/test/java/org/jabref/logic/util/io/FileUtilTest.java

@@ -448,6 +448,32 @@ public void cTemp() {
         }
     }
 
+    @Test
+    void relativizeHandlesSymlinks(@TempDir Path tempDir) throws IOException {
+        assertFalse(OS.WINDOWS);
+
+        Path realDir = tempDir.resolve("real");
+        Files.createDirectory(realDir);
+
+        Path symlinkDir = tempDir.resolve("symlinked");
+        Files.createSymbolicLink(symlinkDir, realDir);
+
+        Path fileInRealDir = realDir.resolve("paper.pdf");
+        Files.write(fileInRealDir, "dummy".getBytes(StandardCharsets.UTF_8));
+
+        Path rel = FileUtil.relativize(fileInRealDir, List.of(symlinkDir));
+        assertEquals(Path.of("paper.pdf"), rel, "Should resolve to simple filename when accessed through symlink");
+        Path fileViaSymlink = symlinkDir.resolve("paper.pdf");
+
+        Path rel2 = FileUtil.relativize(fileViaSymlink, List.of(symlinkDir));
+        assertEquals(Path.of("paper.pdf"), rel2, "Should resolve to simple filename for file via symlink-path");
+        Path outsideFile = tempDir.resolve("elsewhere.pdf");
+        Files.write(outsideFile, "foo".getBytes(StandardCharsets.UTF_8));
+
+        Path rel3 = FileUtil.relativize(outsideFile, List.of(symlinkDir));
+        assertEquals(outsideFile, rel3, "Unrelated files should not relativize");
+    }
+
     /**
      * @implNote Tests inspired by {@link org.jabref.model.database.BibDatabaseContextTest#getFileDirectoriesWithRelativeMetadata}
      */