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We use GitHub Issues. It's very barebones but ties in very nicely with our source control site of choice: GitHub, and there is no need to context-switch.

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I use github issues too. If you prefer the shell over the browser you may want to use this - https://github.com/kashifrazzaqui/github-issues

And on the opposite end of the spectrum, you can find: http://githubissues.heroku.com/

Just looked at this, it looks super useful! Going to try it out.

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