Rename dist -> distance and squared_dist -> squared_distance, enable squared_distance in the modelling language and readd the reference documentation.
Missed %
Fixed header guard issue.
Merge branch 'develop' into feature/add-dist-funcs

Conflicts:
	src/stan/agrad/matrix.hpp
Unified interface for autodiff'ing models
Fix model functional to work with higher-order autodiff by specifying template parameters; add test
Remove domain test for the moment
Merge branch 'develop' of https://github.com/stan-dev/stan into develop
fixes issue #464
added diag_post_multiply to signatures and tested compilability
Merge branch 'develop' of https://github.com/stan-dev/stan into develop
added acknowledgement for bug report
updated command and base_hamiltonian to catch std::exception instead of std::domain_error to catch all Boost math and Stan throws, fixes #476
Merge branch 'develop' of https://github.com/stan-dev/stan into develop
Merge branch 'develop' of https://github.com/stan-dev/stan into develop
added tests for pre/post multiply, fixed bug in post multiply
added pre/post-multiply tests for agrad matrix rev
Move from using a char prefix to string prefix
removed default null character from mcmc_writer and replaced with empty string
Merge branch 'develop' of https://github.com/stan-dev/stan into develop