shuffle: add basic Markov shuffle, other minor cleanups

shuffle: add basic Markov shuffle, other minor cleanups

Add Markov shuffle, which generates Markov sequences with memory of length N
based on the input database.  (N == 3 seems to be roughly equivalent to random
shuffling or reversing.)

Add a report of the overlapping real and decoy six-mers.

All programs now use a common default SHUFFLED prefix and FASTA file reader.