Fulltext file deleted when being renamed to the name differing just b…

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

@@ -223,30 +223,22 @@ public void renameFileToName(String targetFileName) {
     }
 
     private void performRenameWithConflictCheck(String targetFileName) {
-        Optional<Path> fileConflictCheck = linkedFileHandler.findExistingFile(linkedFile, entry, targetFileName);
-        if (fileConflictCheck.isPresent()) {
-            boolean confirmOverwrite = dialogService.showConfirmationDialogAndWait(
+        Optional<Path> existingFile = linkedFileHandler.findExistingFile(linkedFile, entry, targetFileName);
+        boolean overwriteFile = false;
+
+        if (existingFile.isPresent()) {
+            overwriteFile = dialogService.showConfirmationDialogAndWait(
                     Localization.lang("File exists"),
                     Localization.lang("'%0' exists. Overwrite file?", targetFileName),
                     Localization.lang("Overwrite"));
 
-            if (confirmOverwrite) {
-                try {
-                    Files.delete(fileConflictCheck.get());
-                } catch (IOException e) {
-                    dialogService.showErrorDialogAndWait(
-                            Localization.lang("Rename failed"),
-                            Localization.lang("JabRef cannot access the file because it is being used by another process."),
-                            e);
-                    return;
-                }
-            } else {
+            if (!overwriteFile) {
                 return;
             }
         }
 
         try {
-            linkedFileHandler.renameToName(targetFileName);
+            linkedFileHandler.renameToName(targetFileName, overwriteFile);
         } catch (IOException e) {
             dialogService.showErrorDialogAndWait(Localization.lang("Rename failed"), Localization.lang("JabRef cannot access the file because it is being used by another process."));
         }
@@ -284,6 +276,7 @@ public void moveToDefaultDirectory() {
 
     /**
      * Gets the filename for the current linked file and compares it to the new suggested filename.
+     *
      * @return true if the suggested filename is same as current filename.
      */
     public boolean isGeneratedNameSameAsOriginal() {
@@ -296,6 +289,7 @@ public boolean isGeneratedNameSameAsOriginal() {
 
     /**
      * Compares suggested filepath of current linkedFile with existing filepath.
+     *
      * @return true if suggested filepath is same as existing filepath.
      */
     public boolean isGeneratedPathSameAsOriginal() {

src/main/java/org/jabref/logic/externalfiles/LinkedFileHandler.java

@@ -3,6 +3,7 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.StandardCopyOption;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -71,35 +72,38 @@ public boolean moveToDefaultDirectory() throws IOException {
     }
 
     public boolean renameToSuggestedName() throws IOException {
-        return renameToName(getSuggestedFileName());
+        return renameToName(getSuggestedFileName(), false);
     }
 
-    public boolean renameToName(String targetFileName) throws IOException {
+    public boolean renameToName(String targetFileName, boolean overwriteExistingFile) throws IOException {
         Optional<Path> oldFile = fileEntry.findIn(databaseContext, filePreferences);
         if (!oldFile.isPresent()) {
-            // Could not find file
             return false;
         }
 
-        Path newPath = oldFile.get().resolveSibling(targetFileName);
+        final Path oldPath = oldFile.get();
+        final Path newPath = oldPath.resolveSibling(targetFileName);
 
-        String expandedOldFilePath = oldFile.get().toString();
+        String expandedOldFilePath = oldPath.toString();
         boolean pathsDifferOnlyByCase = newPath.toString().equalsIgnoreCase(expandedOldFilePath)
-                                        && !newPath.toString().equals(expandedOldFilePath);
+                && !newPath.toString().equals(expandedOldFilePath);
 
-        if (Files.exists(newPath) && !pathsDifferOnlyByCase) {
-            // We do not overwrite files
-            // Since Files.exists is sometimes not case-sensitive, the check pathsDifferOnlyByCase ensures that we
-            // nonetheless rename files to a new name which just differs by case.
-            LOGGER.debug("The file {} would have been moved to {}. However, there exists already a file with that name so we do nothing.", oldFile.get(), newPath);
+        // Since Files.exists is sometimes not case-sensitive, the check pathsDifferOnlyByCase ensures that we
+        // nonetheless rename files to a new name which just differs by case.
+        if (Files.exists(newPath) && !pathsDifferOnlyByCase && !overwriteExistingFile) {
+            LOGGER.debug("The file {} would have been moved to {}. However, there exists already a file with that name so we do nothing.", oldPath, newPath);
             return false;
+        }
+
+        if (Files.exists(newPath) && !pathsDifferOnlyByCase && overwriteExistingFile) {
+            Files.createDirectories(newPath.getParent());
+            LOGGER.debug("Overwriting existing file {}", newPath);
+            Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
         } else {
             Files.createDirectories(newPath.getParent());
+            Files.move(oldPath, newPath);
         }
 
-        // Rename
-        Files.move(oldFile.get(), newPath);
-
         // Update path
         fileEntry.setLink(relativize(newPath));