fixes spelling of Seq-Gen in HowTo
preparing version 2.1 release
removes externalTheta
fixes bug with parameter parsing
major code rewrite & cleanups
fixes a few bug

+ restores function delete by mistake before
+ passes unit tests
renames variables
simplifies blocks

+ adds caching for log factorials
+ removes unused functions
removes unused functions and updates headers
renames files
updates vignette; ports msFile2jsfs to Rcpp
adds vignette for using jaatha with custom models
ported howtos to knitr
corrects Makefile
corrects a few misspellings
bugfixes in createInitialBlocks
adds citation information
moves howtos out of the package
cosmetic changes
fixes problems from R CMD check