Faster dinucleotide shuffling

Thanks to @atseng95 for PR #109, which greatly speeds up dinucleotide shuffling. This tag also incorporates the change from PR #105 (which has support for supplying pre-generated shuffled references, and was tagged as v0.6.11.0), as well as the small fix in PR #101 (which allows the user to recover if they accidentally set an invalid task index, and was tagged as v0.6.10.1)