added a global marked variable, missing settings, and comments

the JSDoc comments aren't complete but it's a start
Fix sinon-chai "always" language chain
Fix amplifyjs tests by including amplifyjs and jquery definition references
Fix chai-jquery tests
Merge pull request #944 from theodorejb/fix-failing-tests

Fixed amplifyjs and chai-jquery tests
Merge pull request #942 from jedhunsaker/fix-sinon-chai

Fix sinon-chai "always" language chain
Merge pull request #938 from xt0rted/marked

added a global marked variable, missing settings, and comments