Preserve source tree structure with -o option + CoffeeScript source maps

This allows compiling a whole source tree to JS, with source maps if desired, into a new directory with the same structure. (Previously, using the `-o` option would lead to a flat output directory with every compiled JS file.)

The CoffeeScript compilation feature (for ordinary .coffee files) also now respects the `-m` parameter. This closes #176.

Also removes some seemingly useless `loadFile` calls, speeding up compilation.