updated docs for 2.0 for everything but the new command structure
Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
updated for distributions with sampling statements in both definitions and index
added formatting to commands with some extra descriptions
command skeletons in place
outputs optimization to file. fixed by flushing and closing output stream appropriately.
Add return code strings for BFGS optimizer.
BFGS parameter changes.  Add tol_obj, tol_param and tol_grad parameters.  Change stepsize to init_alpha as it better reflects its use.
updated commands after proofreading and fixed in-press ref
pulling out common code
updated return codes for bfgs optimization
Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
added new bfgs args, added syntactic highlighting to argument hierarchy
Clean up BFGS code and messages a bit further.
Merge branch 'develop' into feature/issue-259
Edits for the command argument doc
fixed typos in doc
Merge branch 'feature/issue-211-stan2-manual' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-211-stan2-manual
fixed more issues in manual