Feature/cmdstan issue 4 standalone doc

#### Summary:

No change to existing behavior.
Changes the makefile for building the manual to be more general so it can be included by CmdStan's makefile.

#### Intended Effect:

This should not affect how the manual is built for Stan.

#### How to Verify:

From the command line, type `make manual`. This should still build properly. I've run this on my mac and on the Jenkins machine.

#### Side Effects:

This allows CmdStan to build the manual from its root directory.

#### Documentation:

No changes to user behavior.

#### Reviewer Suggestions:

Anyone.