Include Gromacs files with double quotes in C++ code.

Include Gromacs files with double quotes in C++ code.

Replace #include <...> with #include "..." for Gromacs include files in
all new C++ code.  Also include headers from legacyheaders using
"gromacs/legacyheaders/...".  The C++ code should now compile without
gromacs/legacyheaders/ in the include path.

Updated the include dependency checker with checks related to this
(would have been difficult to find all these places without it).

Change-Id: Ia0fb5f9bc43790619b2dc2027a326c34bb2cf4ca