3.0 - Add missing files to app structure, remove timezone error comments

Follows https://github.com/cakephp/docs/pull/1181 and https://github.com/cakephp/app/pull/42

Also, while we're here:  I kind of want to remove the "Development" section.  It introduces another set of introductions just to say "Oh hey, you can run an app in a subdirectory."  Seems silly.  If that is :+1: I can go ahead and remove it, and patch up the "Production" section to be more collective in either this PR or another one.