make reload spinner fixed, high z-index
Fixed axis link in README
refactor and better document the compiler class

- complete docs for all functions
- move more functionality to private functions
- clean up some difficult to understand and/or messy code
refactors to dynamic content, output path & dirs

- this commit contains a very very edge breaking change, that
  folder_config was removed as an option from app.coffee
- add views and assets to project.dirs
- refactor output path to be more reliable
- port in fix from 8126140d9e for dynamic content
add test mocks for config options
Added command clean, changed readme.md

	modified:   lib/commands/index.js
	Added command clean
	modified:   test/readme.md
	Fixed timeout
	modified:   test/test.coffee
	Added "uncomplete" test
Clean command simplified, test working