Remove proto module as it seems to be unused and causes conflicts in other modules.

The proto module pollutes `Object.prototype` and causes issues with other modules. For example, I am using [connect-assets](https://github.com/adunkman/connect-assets) and wheat together. connect-assets couldn't parse sprocket requires in a JavaScript file because the module [dep-graph](https://github.com/TrevorBurnham/dep-graph) relies on a property called `map` on one of its objects, which conflicts with proto.

It looks like the methods exposed in the proto module aren't even being used in wheat and I've been running a custom fork of the project without it for a few days with no issue.