Fix test runner and regressed tests

If `options.freeVariableChecker` was true then the FromOptionsTransformer returned `undefined` instead of a ParseTree. This caused all the tests to have empty code.

Fixing the above revealed a few broken tests. Most of them were just test errors but there was one  issue with modules. Module instances acquired using `module m from 'name'` are supposed to be live.

Review URL: https://github.com/google/traceur-compiler/pull/487

Closes #487.