Initial commit.
Delete whitespace.
Break lines at 80 characters.
Use pointer to stream instead of reference to stream to allow for null streams
Added write_sampler_state for general implementation display
Don't clear vectors before appending param names and values
Added sample output method
Intermediate reworking of command to use mcmc_writer
Print diagnostic information
Added argument parsers
Argument parsers
Test argument parsers
Recursive arguments
Added many new arguments
New arguments, started refilling command.hpp
Implemented optimization algorithms and various samplers, added appropriate arguments
Merge branch 'master' into mcmc_writer

Conflicts:
	src/stan/gm/command.hpp
Change command name to reflect options besides nuts
Take in unconstrained parameter names when generating diagnostic headers
Fixed creation/use of diagnostic stream, use mcmc_writer for all sampling output