Make emscripten.py run without .emscripten

This is a continuation of the pull request started at ( https://github.com/kripken/emscripten/pull/804 ) except this time it's based against the upstream incoming branch.

At this point, emscripten.py, given sufficient command line options, does not require a ~/.emscripten file.

Now it is suitable for integration into our build system.

Please review!