Use smart pointers for internal memory management.

Use smart pointers for internal memory management.

- Replaced uses of std::auto_ptr with boost::scoped_ptr where memory was
  allocated locally and release() was not used, or refactored the use of
  pointers out completely.
- Use gmx_unique_ptr in containers that are responsible for freeing
  the contained objects.
- Removed an unnecessary #include <memory>.
- Also added doxygen comments in modified parts to satisfy Jenkins.

Part of issue #887.

Change-Id: Ib582b6395fb348d392a742acd4b1ff73acfa74a3