Feature/issue 4 standalone doc

#### Summary:

Splits out CmdStan manual from Stan manual and moves CmdStan manual source to this repo.

#### Intended Effect:

The summary says it all for this repo.

The Stan manual is also getting updated in `stan-dev/stan` to remove the CmdStan portions.

#### How to Verify:

Build it from the new make target.

#### Side Effects:

No. 

#### Documentation:

It's all doc.

#### Reviewer Suggestions:

Daniel.  This should be checked for consistency with how things are going to be distributed as CmdStan.