restored function(){} wrapper around compiled code

This only pertains to JS code is written to a file ("apl -c filename.apl").
renamed some variables to avoid amibuity

code -> jsCode
code -> aplCode
split coffee-preprocessor into two steps

1. Replace each APL fragment with `@FRAGMENTID`
2. Replace each `@FRAGMENTID` with compiled APL code

This should make it easier to insert a third step inbetween, which would
parse the intermediate CoffeeScript code and provide meta-information
about what variables should be available to each fragment.