Sync between RStan and Stan Command-line
========================================

Top-Level Command
Cmd:    stan/gm/command.hpp
RStan:  rstan/rstan/inst/include/rstan/stan_fit.hpp
        rstan/rstan/inst/include/rstan/stan_args.hpp
        rstan/rstan/R/rstan.R

libstan.a
Cmd:    any XXX.cpp file added to makefile
RStan:  rstan/rstan/src/YYY__XXX.cpp


stanc translator
Cmd:    stan/command/stanc.cpp
R:      rstan/rstan/src/stanc.cpp


output analysis
Cmd:    stan/mcmc/chains.hpp
R:      rstan/rstan/src/chains.cpp

var_context impl
Cmd: 
R: rstan/rstan/inst/include/rstan/io/rlist_ref_var_context.hpp 

makefiles
Cmd:    add .cpp files, makefile,  make/make*
R:      rstan/rstan/src/Makefile{,.win}


boost/eigen version 
Cmd:    lib/boost_x.xx.x/, lib/eigen_x.x.x, etc.
R:      rstan/rstan/src/Makefile{,.win} 
        rstan/rstan/R/options.R
