Renamed methods, reordered arguments.
Renamed some method arguments.
More javadoc improvements.
Made AffineTransform's fields private.
Made AffineTransform.inverse() use Matrix3.transpose() instead of Matrix3.inverse().

This works, because we keep the matrix orthogonal and because an
orthogonal matrix's inverse is its transpose.
Fixed some odd whitespace issues with the clone methods.
Moved Matrix3.identity further up.
Javadoc improvements.