Improve include dependency script

Improve include dependency script

- Make the depcheck, doccheck, and depgraphs targets work on the whole
  src/gromacs/ directory.  Now it is possible to run these checks on new
  or reorganized code without touching the scripts themselves.
- Fix the script to correctly recognize relative paths in #include
  directives again.
- Fix some issues the script complains about, and suppress some messages
  within the script itself.
- Make the colors in the module dependency graph somewhat more
  intuitive, and show legacy dependencies in gray instead of bright red
  to make it look reasonable.
- The module dependency graph now includes the legacy modules
  (gmxlib etc.) as well, with a gray background.  This makes the graph a
  bit messier, but still readable (in particular since most of the lines
  to and from them are gray, making them fade into the background).

Now, 'make depcheck' doesn't report any issues, and we should keep it
that way.  'make doccheck' (with the current, somewhat relaxed rules)
reports only a few issues that should be relatively easy to fix, but
left those for separate changes.  Other Doxygen documentation checks
(not only about file dependencies) could also perhaps be included in
this same target.

Change-Id: I3f837c69f2608d2a6a25ed4062102d252a85a0cf