Module dependency cycle checker for 'doc-check'

The doc-check script now also checks for cyclic dependencies between
subdirectories within libgromacs.  Currently, this reports 247 cycles,
out of which 210 contain a legacyheaders->swap edge.  Update the
documentation for the checker.

Add a separate suppression mechanism for cycles.  With some changes in
the way the cycles are reported, the existing suppression mechanism
could also have been used.  However, this separate mechanism allows the
same information used for layout of the dependency graph, such that the
ignored edges causing cycles are also ignored in the dependency ordering
of the modules.

Change-Id: I7b9ed3cd0d5ed05dee8902f96b2407a113f4b200