Update doc to mention 2.2.0 instead of 2.1.1.
Rename old f3x4_matrix to muse_gaut_matrix, since that is what it is.
Add prefix for F1x4 and MG94 nucleotide models.
Rename prefix from n -> Siten for nucleotide models in MG94w9.
Switch to using --model rather than --BUGS
Update documentation.
Fix F=uniform.