Simplify the cram_decode_slice_xref code given we now know it's
executed on each and every sequence in the slice before attempting to
convert to BAM. This means we don't have to fix up mate information,
only our own information.

In doing so this also cures a bug with template triplets (1st, 2nd and
one other) introduced during the move to cram_decode_slice_xref().
Added -C/-D options to usage.
The mind bogglingly daft combination of embedding references for
non-position sorted data now works, albeit tragically inefficiently,
rather than simply core dumping.
Fixes for handling name sorted data. The template length and sign
(+/-) calculation assumed data was in position sorted order. This is
no longer the case.