Deprecate Matrix4.getPosition() and replace all usages in core lib.

I saw this bug from @WestLangley:

https://github.com/mrdoob/three.js/issues/2967

In response I decided to do the work to fully deprecate Matrix4.getPosition() by removing it from usage and also adding a proper deprecated log message.

@WestLangley, can you verify I didn't make any mistakes while implemented your feature request?