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)

Using c++11 to initialize the map instead of calling a function everytime

I removed many cases that are not in practice useful. In particular,
it won't be anymore possible to:
- Link statically PLUMED if both "ar" and "ld -ro" do not work correctly.
- Link runtime PLUMED is "ar" does not work correctly.

Both statements are true only for installed PLUMED. Not installed plumed
still uses object files.

(see #352)

Notice newer cppcheck versions are slower. In order to make the check fit
on travis-ci I had to make a few extra changes:
- better optimization flags when building cppcheck
- force a number of ifdefs in the check

Now master takes approx 25 minutes, so we have room for adding new code.

just annoying when there are directories whose name contains a space
within the src/ directory

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.

Currently, a lot of dummy headers are installed such as
plumed/core/tools/Tools.h
in order to allow including tools from core. I made a script that
edits the include files when they are installed so that the extra
files are not required.

faster implementation, calls scripts once

added comment in config.txt file

Can be retrieved with

plumed config mpiexec

While doing plumedcheck, verify that autoconf has been applied correctly

Three versions are installed:
plumed - flags to link plumed (as in patch --shared)
plumedWrapper - flag to link plumed wrapper only (as in patch --runtime)
plumedInternals - flags to link full plumed library, including required CPPFLAGS

Notice that some macros are stripped from CPPFLAGS. This might
be improved in order to keep only the relevant ones.

This library contains only the wrapper/Plumed.o object and
can be used to link plumed with --runtime option without
incurring in linking errors when the MD code links PLUMED_LOAD
variables more than ones

@valsson @giovannibussi could you double check that?

this could be removed by doing the following:

- applying astyle to src/lepton
- fixing namespace used in src/lepton/*.cpp files

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.

This requires a few fixes:
- Replace -ansi with -std=c++11 in autoconf.
- Add a check that c++11 is supported in autoconf.
- Change flags for cppcheck.
- Remove travis configurations that would fail.

Additionally, I removed the check for 'explicit' keyword,
which is not needed with C++11.

Fixes #212

maketools/cppcheck has been renamed into maketools/codecheck

To use it:
make cppcheck only runs cppcheck
make plumedcheck only runs plumedcheck
make codecheck runs both and aggregate messages (to be used e.g. on travis)