shouldBe() transformation does not work if opt_tolerance specified

[dmorejon]

Although shouldBe() is usually called as: shouldBe("actual", "expected");, the function supports an optional
tolerance value, such as: 'shouldBe("actual", "expected", tolerance);, then our transformation to assert_equals(actual, expected);` would be incorrect.

This is should be relatively easy to fix, but is a more general issue of dealing with optional parameters in js-test.js functions. We need to remove these parameters before transforming to testharness.js functions, since we usually update the arguments array in place (meaning the third parameter would still be present if the testharness.js function only has 2).

These mistakes would fail verification, so would hopefully be caught by the person running the tool.