old fixes
update sphpdox and dependencies
add untracked files from previous update
fix array to string conversion. add api dirs
Wholistic redo for Omeka 2.2, and updating all the scripts.

Updates sphpdox
Updates hacks into sphpdox hacks for sane(r) path handling (this and above probably should've been separate commits)
Looks like handles libraries/Omeka better, but still work to do on models and views
Still redo work to do for packages handling

The new separate buildIndex method in sphpdox code should make it easier for us to glob in the subdirectory index and/or other files.

Added some high-level things to let us grab the reflections, which I hope will let us handle Interfaces better

(Ping @zerocrates so he knows this exists)