I do not plan to enable code coverage automatically with a html file. When a user uses their own HTML file I just honor what they have set in theirs. That said Chutzpah is able to (with a tiny bit of work) run tests which use Require.JS. Take a look at https://chutzpah.codeplex.com/SourceControl/latest#Facts.Integration/JS/Code/RequireJS/all.tests.qunit.js for an example.
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