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)

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

made version in "plumed config" consistent with the change
done in 2e4cee92

Notice that this also affects the git version reported in plumed log

[makedoc]

This is a textual file that contains all the configuration info.

It should be easier to parse from scripts.

- Implementation of short help (with :PHelp)
- Updated doc
- Autocompletion now knows if label was already provided at the beginning
  of the line and does not suggest it anymore in case
- Compilation of the vim plugin is more similar to compilation
  of the user doc
- Compilation of the vim plugin is made when doing "make install"
  from root dir.

- Made plumed dictionaries local to buffer
- Improved syntax annotation
  Now it also annotates spaces. Moreover, output is formatted.
  (requires a rt to be reset)
- Fixed nested parenthesis
- Made all regions foldable (include {})

allows syntax to be checked