Regular patch command verifies if the previous version from the patch file matches the file being patched. If there are differences, the patch is not applied and the user is notified. JDiff applies the patch blindly that makes it dangerous to use.
Desired behaviour: make a check of contents before applying the patch. Stop applying the patch and point to the conflicting lines. Be smart to handle different line endings in patch file.
Checked on r22076, unified patch.