Fix utils docs and affine

I think this should address https://github.com/nipy/dipy/issues/322 and https://github.com/nipy/dipy/issues/351.

Because I had to move most if `_utils` back into `utils`, sorry I'm the one who broke this in the first place, this PR might seem like a lot, but it should be easier to review by looking at the individual commits. The first two commit are pretty strait forward and the third commit is pretty much just a copy and past.

@jchoude could you take a look at the functions that use the `affine` argument and see if we could make it any more clear in the docs that this argument is required.