Updated makefile dependencies for auto-generated cpp files

#### Summary:

Make dependencies now work through the parser for automatically generated C++ from Stan programs.

#### Intended Effect:

Fixes broken *test* behavior, not code behavior.

#### How to Verify:

`make src/test/test-models/good/io_example.cpp`
`make src/test/test-models/good/io_example.cpp`
(should do nothing the second time)
`touch src/stan/version.hpp`
`make src/test/test-models/good/io_example.cpp`
(should rebuild the parser and a new io_example.cpp)

#### Side Effects:

None.

#### Documentation:

None. Not user facing.

#### Reviewer Suggestions: 

Anyone. Should take < 5 minutes to verify.