Update some installation-related docs
- Add comments for installation-related variables in CMake, in
particular the RPATH section that has caused some confusion.
- Document those few variables that can be used to alter the
installation tree structure in the install guide.
- Reword some parts in the install guide about CMake iteration.
- Remove GMX_INSTALL_PREFIX, as there are other approaches to get the
desired result with CPack that are less confusing. This variable
wasn't documented or probably used anywhere outside some dormant
Jenkins jobs.
Change-Id: I199b06d905b45961313ed9fa44ae82e5987be0fe