I have been working on a project with on Github and we are using Waffle.io to organize our issues on an agile board. One bad thing about Github is that it not always apparent what issue a commit resolved. To add context to commits I have begun appending the issue number to commit message. When viewing the commit in web interface of Github, it will automatically link to the issue. To accomplish this, I use commit that take the form of "This is my first commit [issue #123]"
. Obviously, this process can be automated.