The used modules were not detected correctly on travis probably due to
some settings for the cd option. This was harmless since the list of used
modules was not checked indeed.

required fixing some incorrect escape sequence in plumedcheck

closing files to avoid too many open files

Allow deprecated header in Plumed.h (needed for next commit)

I allowed include commands such as #include "../module/file.h",
only in the case where module is an used module (or the current module).

Later I would like to see if it is possible to eliminate
the "make links" stuff completely.

(still a stylistic warning)

Check first if astyle is present. In this way, when astyle is not compiled,
we get a single error instead of one error per file.

While doing plumedcheck, verify that autoconf has been applied correctly

@valsson @giovannibussi could you double check that?

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

Travis-ci job doing cppcheck also checks whether astyle
has been enforced.

See #215

- Vim syntax for the awk file
- Some information is given once per file now.
- Registration of vessels and metrics is also logged.
- Check that .h files do not include:
  * inc files (they are temporary)
  *  external .h file (they might be not available when using plumed library).
The latter is only notified now, since it must be accepted for mpi.h
- Separately store documented actions/cltools/other.
- Check that module type is correct.
- Extensive doc for each check added.

I added a awk script src/maketools/plumedcheck
that works similarly to cppcheck. It takes as argument
a list of files and analyze them.