generate hpp from Stan file

#### Summary:

Stan programs are translated to `.hpp` files for testing. They used to be `.cpp` files.

#### Intended Effect:

`foo.stan` is compiled to `foo.hpp` instead of `foo.cpp`
The `clean` targets have been updated.
Includes using the old `.cpp` files have been updated.

#### How to Verify:

The tests should still run.

#### Side Effects:

These only affect tests.
You might have to run
`git clean -d -x -f` 
after the merge to remove the old generated cpp files. Or, run `make clean-all` before merging.

#### Documentation:

None. I searched the Stan doc for references to the generated cpp, but we moved that into CmdStan. That will need to change appropriately.

#### Reviewer Suggestions: 

Anyone. Given that it's make related, just scan to make sure there isn't anything ridiculous in there.