Update Loader.js

Changes 1 KB = 1000 B to 1024 KB = 1024 B
Adding boolean attribute "transparent" for files with transparency. 

http://stackoverflow.com/questions/18444939/define-transparent-material-in-json-model-format-3-1
Update CubeGeometry.js

warning the user
Update build.js
Update WebGLRenderer.js
Update Geometry.js
Update WebGLRenderer.js
seems like I forget a underscore
refactors editor menubar as preparation for undo/redo mechanism
removes usage of with keyword du toe performance issues

http://jsperf.com/with-statement/4
Merge branch 'patch-3' of https://github.com/gero3/three.js into dev
r67dev
Simplified WebGLRenderer's initDirectBuffers.
add the stuff for buffergeometry
WebGLRenderer: Explicit checks for extensions.
Minor clean up.
Merge branch 'patch-3' of https://github.com/gero3/three.js into dev
WebGLRenderer: Saving type of TypedArray in geometryGroup.
@gero3 what do you think?
Code clean up.
Updated builds.