softmax unfolded rev mode, added log_softmax and unfolded rev mode
added log_softmax rev mode
all tests passing for softmax functions and categorical distributions
finished merge vs. new Boost, fixing matrix includes
generalized optional dimensions to sequence of dimensions to allow double-indexing on LHS of assignment
test for new statement grammar indexing
more throrough assignment indexing test
updated .gitignore, make/tests, and base_hmc_test to not show the improper artifacts as tracked in git
removed categorical_log, added vector/matrix log_sum_exp, improved categorical_logit speed when not vectorized
merged with develop, resolved conflict in function_signatures.h
Merge branch 'develop' of https://github.com/stan-dev/stan into develop
added cholesky_factor to ast, grammars, code generator
added checks for cholesky and lower triangular
added cholesky factor transform to prob/transform.hpp with tests and some extra error handling cleanup
added reader and writer for square Cholesky, which is now feature complete and unit tested
finished merge
Fix spelling of "gaussian"

Change spelling of "guassian" to "gaussian" in a couple of places; at
least one of which is important.
support for rectangular cholesky factors for covariance
added square Cholesky factor declaration form with only one dimension
updated manual with cholesky_factor_cov type syntax and transform definitions