Clean up the contents of the generate folder

Did a few things here. 
* Moved files around so that all of the combyne stuff (templates, partials, etc) are in a folder, all of our input json is in a folder (vx.x.x.json, descriptor, etc), and the scripts are in a folder.
* Renamed the generation scripts to generateJson, generateNativeCode, and generateMissingTests
* Changed the index of generate to run all 3 other generate scripts
* Renamed utils.js to helpers.js, and moved some things from there and util/file.js into a new utils.js
* JSON output (idefs.json and missing-tests.json) are now output to generate/output/