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.