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.

- Cleaned up log reporting and issue identification

- "Fixed" the global navigation, now that globals are displayed .. now
  just need to fix the documentation the members aren't incorrectly listed
  as globals ..
Merge pull request #1332 from pnstickne/wip-docgen2

Documentation - YUIdoc to jsdoc, global nav