Haven't tested if the box.addPoint decreases performance...

Misteriously when using the latest version of the lib on the project I'm working on I'm getting this error:
> Uncaught TypeError: Object [object Object] has no method 'set'
This is caused when THREE.UniformsLib.common.diffuse initialises a THREE.Color (THREE.Color.set() seems to be undefined then).
For some reason this only happens when I load Box2D before three.js. If I load it after is all good. But this fixes the problem too.
/ping @bhouston

fix three missed conversions to closures.  switch to extending math prototypes rather than replacing them.  This is to ensure that types created in closures within a type's prototype definition get their prototype updated with the full definition.

Changed back some .projectPoint() to .applyMatrix4() as per bb873d16.

@WestLangley I've changed most of the vector.applyMatrix4() to vector.projectPoint().
Feel free to change back the ones that aren't needed (or let me know which ones can need to be changed back and I will do it).

update math constructors to not copy when provided explicit initial values per @mrdoob: https://github.com/mrdoob/three.js/pull/2902#issuecomment-11999928

Removed Vector* add() to addVectors() and addSelf() to add(). Same with sub, cross, min, max, lerp... Renamed Matrix* and Quaternion multiply() to multiplyMatrices(), multiplyQuaternions() and multiplySelf() to multiply(). See #2860.
Good thing we have a ton of examples to make sure nothing is broken. The unit tests also helped. However, I suspect I've left something unchanged.

Also, code clean up here and there.

Add missing space
Fix isIntersectionSphere
Addunit test for isIntersectionSphere

Tets if two spheres intersect

Renamed .multiplyMatrix* to .applyMatrix* and .multiplyQuaternion to .applyQuaternion as suggested by @WestLangley in #2860.

Makes the code so much nicer imho...

add Triangle3, add optionalTargets to Box2,Box3,Plane,Sphere,Ray where possible to reduce GC load, add Triangle3 unit tests.

More garbage collection friendly (on repeated calls) Geometry.computeBoundingBox() and Geometry.computeBoundingSphere()

fixed #2728, Moved geometry primitives out of src/core into src/math.  src/core is now exclusive scene primitives.

add equals, clone to Box2, Box3, Plane and Sphere. Adopt +Inf/-Inf in Box2 and Box3 per @mrdoob'd recommendation.  Begin Box3 unit test.

move away from static fromXXX-style constructors to setXXX style member functions widely used in ThreeJS.