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I'm actually not sure if its my default browser for ubunutu that I need to change or just for Thunderbird. I wasn't aware that I could have a default browser for ubuntu but I use firefox and thunderbird opens everything in chrome.

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Go to System -> Preferences -> Preferred Applications

Got this from here - http://tips.webdesign10.com/how-to-change-the-default-browser-in-ubuntu-linux

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http://appnr.com/package/galternatives GAlternatives lets you set default browser, this solved the problem for me, some apps still opened firefox instead of chromium after setting the prefered browser via ubuntu menu

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