Open files in binary mode, where appropriate.

Should have been doing this all along, as Python's default I/O mode is
text mode.  It won't make any difference in most cases, perhaps all,
but binary mode is certainly correct if we're being careful.

* onetime
  (Pad.__init__): Read the pad in binary mode.
  (Configuration.save): Add comment explaining why not binary mode.
  (main): Open input and output in binary mode.
* onetime
  (Pad._make_fuzz): Explain why we read 4 bytes.
  (PadEncoder.encode): Remove old comment.
Update pad consumption when doing the new fuzz skipping.

This fixes a bug introduced in commit 52e24e550 that would result in
re-use of pad data.  This also makes some regression tests start
failing, because the used lengths they're expecting are now different;
I will fix the tests in a subsequent commit.

* onetime (Pad._make_fuzz): Adjust pad used length.  I mean, duh.