Fix a bunch of dumb bugs in nacl-sdk module.

* Need to clone option objects, not just reuse them.
* Return early from getToolPath when the tool is already in the hash.
* Change ";" to "," in a couple of places. Previously this would define
  global variables, instead of local variables. :-(

  var foo = blah;
      baz = stuff,
  ...
Add default include paths to naclbind-gen

Also add option for setting the moduleName from naclbind-gen
Add rot13 integration test