Add index of functions to the TOC of the reference manual
Snap final var/covar adaptation window to warmup period
Made initialization warning less verboe and, hopefully, more clear
updating Eigen library from 3.1.2 to 3.1.3
updating covar adaptation test
updating covar and var adaptation test
fixed false positive in warning for transformed parameter sampling
added operators for warning test for transform
Merge pull request #32 from randommm/indexTOC

Add index of functions to the TOC of the reference manual (thanks -- I missed it when I created the index)