From #1454, small edit to TrackballControls.js to zoom properly with an OrthographicCamera
Created a `TrackballControls` for `OrthographicCamera`
Removed `checkDistances` and associated variables
Adding boolean attribute "transparent" for files with transparency. 

http://stackoverflow.com/questions/18444939/define-transparent-material-in-json-model-format-3-1
Examples: GPGPU Birds BufferGeometry

- replaces old geometry with a buffergeometry
- this helps speed up initialization times
- also renamed SimulatorRenderer -> SimulationRenderer
Examples: GPGPU Birds update BufferGeometry addAttribute method
SpotLight: added shadowCamera parameters to clone() method
Examples: GPGPU Bird, removed redundent variables in shaders
DirectionalLight: added shadowCamera parameters to clone() method
Rename Matrix*.multiplyVector3Array() to Matrix*.applyToVector3Array()
TransformControls: fix incorrect application of applyProjection()
can cause problems if object and datablock names are different
Update BufferGeometry.html

fixes typo
Merge branch 'dev-dir' of https://github.com/WestLangley/three.js into dev
Merge branch 'dev-multiply' of https://github.com/WestLangley/three.js into dev
Merge branch 'dev-trans' of https://github.com/WestLangley/three.js into dev
Merge branch 'dev' of https://github.com/anka-sirota/three.js into dev
Updated builds.
Merge branch 'gpgpu_birds_buffer' of https://github.com/zz85/three.js into dev

Conflicts:
	examples/webgl_gpgpu_birds.html
Fixed a typo.