Compare the contents of two files (xml or properties in my experience) that are similar, putting the contents of one on the clipboard and selecting the other in the editor in the normal fashion. The files should be nearly identical apart from one of the lines of the clipboard side having some extra spaces on the end of the line. Assuming the destination file is writable, and you are comparing with "Do not ignore whitespace" , you should be able to press a right-arrow button in the mid-margin to overwrite the line in the destination file with the source version (which has the extra spaces on the end). Now close the comparison pane and save the destination file. Now do the compare again. You will notice that you are back to your original situation, because the extra spaces were not saved.