stepwiseqtlF: Further revisions to get covariates to work
A bunch of big changes simplifying arguments

 - We're focusing just on the normal model, so we can get rid of maxit
   and tol in many cases. (And I don't think we need to make the
   tolerance for lmfit an argument.)

 - Also, simplified the arguments to refineqtlM and refineqtlF by
   forcing the use of a qtl object (vs providing chr and pos arguments)
Nearly fixed stepwiseqtlF; also making method="hk" the default
refineqtlF.R: revise indentation in file
refineqtlF.R: small simplification
refineqtlF now working with covariates
Update version + date
Fix a small problem I'd introduced for case w/o covariates
Merge Karl's changes