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
Move gstat.h to gmxana/

Remove unnecessary inclusions of gstat.h from outside gmxana/.
Now that the header is no longer used outside gmxana/, move it into that
directory.  Still install the header, since it contains a wide mixture
of stuff, some of which may actually be used by user tools.

This cleans up the include dependency graph considerably, since the
legacyheaders/ directory no longer depends on commandline/.  This was a
source of a cyclic dependency that made the graph layout very confusing.

Change-Id: I3843f2773d6b393e4d260e84478ab559ab8e00d7