Feature/issue 325 manual 2.1

#### Summary

Manual changes for 2.1.0 release.  Finishes issue #325 (sorry, feature branch is named wrong)

#### Intended Effect

Get manual into releasable state for 2.1.0.

#### How to Verify

Painstaking comparison with previous manual and issues listed in #325 

I don't think anyone else needs to do this.   There's one issue from Daniel that he needs to check because it looked OK to me before I tried to fix it --- maybe Michael had already fixed it.

* [x] In commands.tex, in "Command-Line Option Examples," the multiple figures needs to change. Most of the manual is written with the same assumption I've made: on any valid Stan run (whether it's optimize or sample), it will echo the parameters. (I don't understand the intent of this change, which is why I haven't done it). I don't see how the examples relate.

#### Side Effects

None.