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* Uses option arguments instead of positional ones.
* Allows linking to dlmalloc.
* Accepts both .bc and .ll files and takes care of annotations.
* Allows running the LLVM optimization pass automatically.
* Updated test runner to use the new emscripten.py interface.
Refactoring:
* Moved settings.py to root folder. It no longer applies just to tests.
* Updated references to settings.py.
* Added an __init__.py to tools, so we don't have to hack around imports.
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