The editor of our submitted paper asked for a red-lined article file. Using latexdiff makes this task very easy: Simply grab the 2 versions of your manuscript and issue
latexdiff manuscript_v1.tex manuscript_v2.tex > diff.tex latexmk -pdf diff.tex
. The latexmk program allows to get all necessary passes to get a clean output file.
One issue is that one version imported a few other source files using the \input command, so we used the following parameter:
latexdiff --flatten manuscript_v1.tex manuscript_v2.tex > diff.tex latexmk -pdf diff.tex
it is recommended that instead of using bibtex, you copy and paste the content of the .bbl file.
Moral: one advantage of LaTeX is that your data, your dear prose, is in text (not binary) format and has an open syntax. This process allows the creation of the red-lined article file in one shot with no fiddling and lost time of copy and pasting. So whatever soft you use to put your ideas in readable digital format, just use something simple, structured and open.