Clean up the contents of the generate folder

[maxkorp]

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/