How should I highlight extensive changes in a revised manuscript? I revised and resubmitted my manuscript (rejected with the chance of resubmission) to the same journal. I listed all my answers to the reviewers' comments at the beginning of the document. Later, the editor asked me to highlight the changes in the text to make it easier to track them. Since I almost rewrote the entire paper (I mention it in the resubmission letter), about 85-90% of the text would be colored.

I have two questions:


Should I fulfill the editor's request even if almost the whole manuscript turns into let's say red? I'd prefer yes.
Should I place color tags in the Latex source file, or should I highlight changes directly in the pdf file? Which of these or even other choices are the most appropriate?
If the editor's already asked you to highlight the changes, then you should highlight the changes even if it's 85-90% of the text.

As for color tags, it's up to you. Both are equally good. I would highlight on the PDF since I find it easier to do, but if you prefer color tags that's just as good. Be sure to pick a color like red or blue - something that makes it easy to discern the changes from the rest of the text.