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
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
slight doc cleanup for transform.hpp
fixed one more misspelling of Guassian
Merge pull request #165 from stan-dev/feature/issue-149

Addresses artifacts created by base_hmc_test: src/test/mcmc/improper and samples.csv
Merge pull request #168 from stan-dev/feature/cholesky_factor_type

Feature/cholesky factor type
Merge pull request #167 from pdmetcalfe/bugfix/gaussian-typo

Fix spelling of "gaussian"
Merge pull request #163 from stan-dev/feature/issue-159

Fixes #159.
Merge branch 'develop' into feature/increment_log_prob

Conflicts:
	src/stan/gm/ast_def.cpp