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Yah, we're fighting this too. We have back and forth with various devs on our team - some use github, we all have to use Tracker.

Just curious as to what you think Github could do to fix this. I have a list of wishes and I'm always curious what other people have.

GitHub + ZenHub work great.

* ZenHub - Agile GitHub Project Management Software || https://www.zenhub.com/

GitHub + Marker for bugs.

* Marker - Visual Feedback & Bug Reporting Tools for Web Professionals || https://getmarker.io/

GitHub + Unito + Asana even... for clients to get some pretty dashboards without getting bogged down... this works great too.

* Unito - Connect your project management tools and become your team's collaboration hero || https://unito.io/

I love how many things play nice with GitHub now.