I love GitHub. I put all my code there. Github for Mac is a very nice Git GUI. And they even integrated a basic and powerful Issues Tracker. But it's pretty hard to find the documentation for it.
Issues are attached to a repo. It is a tool to track issues (bugs, features missing, bad text etc) for that repo. It is both a web application, and it has links to your commit messages, and there's an iOS application. It helps you track, comment and prioritize these issues.
Basically, you log those issues using the web interface or the iOS application. Then, when you solve the issues, you can add commit messages that automatically close your issues. To reference an issue, just add
fix #1234 or
close #4567 in the commit message where 1234 is the number of the issue. For example
git commit -m 'Corrected the gps. fix #238
You can create Milestones and assign issues to milestones, you can tag issues, assign them to someone etc.
It's possible to give access to your clients on the repo and the issues tracker. That will help you communicate with the client.
If you want to read the original documentation, there's apparently only this and that.