This guest blog post is brought to you by Nuno Pinheiro, the author of a Chrome extension for navigating to your issues from a GitHub commit/PR page. Please post your questions as comments below, and the author will address them.
When assessing the issue tracker to use in a project, if the project is hosted on GitHub, it is really easy to start using the GitHub issue features. It is configured out of the box, and your commits and comments can have hyperlinks to your issues if you refer them. But if you are developing the project professionally, you will probably want to use a more powerfu