The material by Matthew Gentzkow and Jesse Shapiro is found here. This uses Stata, but the principles are general. Course material on "reproducible research" can be found here. An introduction to Git and GitHub for social scientists is here.
I briefly mentioned ShareLaTeX at the beginning. I also discussed a paper with David Larcker and Peter Reiss. The GitHub repository for this can be found here. The GUI software I was using was SourceTree.
With regard to a more recent JAR paper (I did not discuss this one today), the code and data that I was responsible for can be fo