updating makefile help
adding makefile targets to build the Stan user guide and the CmdStan guide
created CmdStan doc from Stan manual
updated parallel instructions to remove backslash
emphasized need for PATH update and check in Windows install
more updates to clarify arguments based on issue in stan issue tracker
updated makefile for new doc and stan sub-module
updating Stan version
updated stan
updated Stan doc
Merge pull request #15 from stan-dev/feature/issue-4-standalone-doc

Fixes #4. Feature/issue 4 standalone doc