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So I changed a lot here and am not sure if this is the direction you want to take the project...
Initially I wanted to clean up the build and get things setup to be on npm so it would work better with the browserify workflow as well as pave the way for a test+benchmark suite I am about to work on for opal.io (noticed problems in Safari 7.0)
A few keypoints:
scryptis the exported module and has ascrypt.create(total_mem)function for exposing the factory.My Makefile chops are probably not the smoothest and I am not super familiar with working with emscripten. The diff of my compiled version of srcypt was different than the one you have but I am assuming emscripten picks random var names etc.
Let me know if you want me to change anything. Thanks for making this available :)