When writing papers (and even more - when revising after collaborators', or reviewers', remarks) it's hard to keep track what is done, what needs to be fixed, what cannot be fixed, when opinions of authors are equivocal (and when an issue raised by one author is not supported by the others).
Moreover, it generates to a lot of e-mail traffic, often with a short remarks.
The question is, is there a issue tracking software (or workflow) suitable for reviewing academic papers?
(As a side note, I'm familiar with JIRA, but never used it for papers. I'm the most interested in answer when someone actually uses a given method, not "well, I never tried but here is [a link to a random issue tracking software]".)