Merged master, preserving development code in mcmc and gm
Merge branch 'master' into hmc_refactor

Conflicts:
	src/stan/gm/command.hpp
	src/stan/mcmc/adaptive_cdhmc.hpp
	src/stan/mcmc/adaptive_hmc.hpp
	src/stan/mcmc/hmc_base.hpp
	src/stan/mcmc/nuts.hpp
	src/stan/mcmc/nuts_diag.hpp
	src/stan/mcmc/nuts_massgiven.hpp
	src/stan/mcmc/nuts_nondiag.hpp
	src/stan/mcmc/util.hpp
	src/stan/model/model_header.hpp
merge master to fvar
Merge branch 'master' into fvar
merged conflict in cloglog
added revised cloglog test
Merged hmc_refactor
rstan: add point_estimate_Nesterov
Merge branch 'master' of https://github.com/stan-dev/stan
Merge branch 'master' of https://github.com/stan-dev/stan
Merge branch 'master' of https://github.com/stan-dev/stan
rstan: change upon merging brach hmc_refactor (not finished)
Merge branch 'master' of https://github.com/stan-dev/stan
rstan: get_cppo return visible list
rstan; add nesterov optim (bfgs not added so far)
rstan continued work for the merge of hmc_refactor
Merge branch 'master' of https://github.com/stan-dev/stan
rstan, add epsilon jitter
Merge branch 'master' of https://github.com/stan-dev/stan
Merge branch 'master' of https://github.com/stan-dev/stan