Documentation - YUIdoc to jsdoc, global nav

- Added support to deal with some of the YUIDoc "formats" used to
  represent arrays. It covers the case of the old PIXI documentation
  (The PR for the critical pixi changes has also been accepted, whoot!)

- Cleaned up log reporting and issue identification - less total messages = higher percent relevant messages.

- "Fixed" the global navigation, now that globals are displayed .. now
  just need to fix the documentation the members aren't incorrectly listed
  as globals .. all documentation except for incorrect "@klass Rounded Rectangles" from Phaser.