(PS: why cannot I reply to paulrouget's message?)
http://ditz.rubyforge.org/ http://pitz.tplus1.com/ https://github.com/jeffWelling/ticgit http://www.bugseverywhere.org/
... and probably others. That's just based on a quick Google search.
One nice thing about this approach is that your issue's state follows your code through merges. When you fix the bug you mark it as 'fixed' and commit that change to a branch. When it gets merged into master, the 'fixed' status gets merged as well.
An org-mode file named 'issues,' with each issue under its own heading?
A directory named 'issues,' with an org-mode or CommonMark file for each issue?
A directory named 'issues,' with a directory for each issue, with CommonMark, org-mode or restructured text files for each person's comments?