Last week, we got reviews back from eLife on the "Integrating influenza antigenic dynamics..." paper. Fairly positive, but as always, there are a number of issues that need correcting. Mainly to help organize the process of responding to reviewer criticisms, I've tried to treat criticisms as "issues" that need fixing like bugs in a piece of code. All the reviewer criticisms are now up as issues on GitHub. As I work, I'm closing issues by linking to a commit that fixes the issue in the text, making it clear what, exactly, has been revised in the text in response to each criticism.
I'm convinced that issue tracking is a good model for the process of correcting particular scientific issues with a manuscript. I could even imagine a manuscript publishing pipeline that gives reviewers the ability to create and close issues. This would thread manuscript conversations by topic rather than exchanging long point-by-point response documents.