Add beginnings of new developer guide
Devel guide: Outline of things to add, regarding data and file formats
Add sample data files (from Moore et al 2013, Genetics 195:1077-1086

 - Also suggest the yaml package
 - Omit microbenchmark package
Fix a few things in .Rbuildignore; was including Notes, *.html and *.Rout
simplification of .yaml file for sample data
Additional files to sample data files & script to create them
Yet another fix to sample data files + script generating them
Initial work on read_cross2
test-hmmbasic-ri*.R: small changes in comment strings
hmm for bc/f2 X chr: true genotypes using "full" encoding

 - Instead of having 3 possible genotypes on X chr in backcross and 4 in
   intercross, use codes that split the males and females (and the two
   directions among females, in the intercross), so that we won't have
   to do any rearrangement afterwards

 - We *will* need to subset the genotype probabilities, as if there's
   only one sex (or only one direction, in an intercross), the genotype
   probabilities on the X will have some columns == 0

 - My idea here was that I can then have a helper function in c++ that
   will return genotype names, given the vector of allele codes
Update version + date
Revise column name in sample phenocovar data file
revise yaml format to have genotypes give explicit encodings
Another adjustment to grav sampledata
sample data: add '-' as possible missing value
read_cross2.R: initial draft
read_cross2: output to have class "cross2"
Remove sampledata; I'm going to re-do it using the 2nd replicate
New sample dataset: 2nd replicate from Moore et al (2013)
sampledata: Revise comment in yaml file