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.

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

Includes both syntax and autocompletion

The new message class (information) is treated as (style).

I temporarily add two travis test to allow 1.71 to fail.

Defining a capitalized enum was useless in the end. I now use
cmd_string
as the name of the enum, where string is the string for the
cmd interpreter

Enum list and word map are now generated with a script.

To add a new command it is sufficient to add a case command as:

case PIPPO: // cmd pippo

It is related to #182, though I let the issue open since I think
we should automatize also the cmd documentation.

ask for confirm before deleting files

Fixes #157

Now configure properly takes into account paths such as
--bindir=/path
etc

This implementation hardcodes all the path into the
src/config/ConfigInstall.cpp file. I followed the instructions on autoconf
documentation so that the paths can be changed at install time using e.g.

make install prefix=/path bindir=/path/binxx

This should be the standard behavior.

I removed the possibility to use PLUMED_SUFFIX and PLUMED_LIBPREFIX
since it was a bit too difficult to maintain.

I significantly simplified the src/lib/Makefile by using
the standard directory names for autoconf.

Instead of replicating the whole tree upon install,
now objects are copied to prefix/lib/plumed/obj
and assigned a number.

When possible, objects are grouped in a single kernel.o
with ld -r (tested in configure). This saves a lot
of disk space.

I also removed from the install directory some other
useless files.

The Plumed.inc/cmake files when installing
are generated in a different way from the ones
used prior to installation. Thus, to avoid too many
repetitions, I wrote a small awk script the transforms
Plumed.inc to Plumed.make

Using "_" instead of "-" to avoid clashes.

Actually, the problem was that doing
make install PLUMED_SUFFIX=2
make install
The second install would have canceled the executables installed
by the first install. This is because install assumes names such as
plumed-* to be scripts installed for cross compiling

This is replaced by ./configure --enable-modules

Includes statistics of (style) warnings.
Can be used to see if the number of warnings decreases.

Apparently with the changes in the CPP macros cppcheck
now scan the whole blas/lapack source and complains.

I removed these complaining from the fatal ones

Added support for DESTDIR

We usually allowed users to customize the name of the plumed
library using env var PLUMED_LIBSUFFIX. I changed it to the
standard autoconf behavior, that is using
--program-suffix
--program-prefix
at configure time.

PLUMED_LIBSUFFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

This makes it compatible with the standard behavior of GNU tools.

PLUMED_PREFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

I invoke cppcheck from an external script that makes the reporting better.

In particular, I show "fatal" errors at the end, where "fatal" means
all reported issues with the exclusion of "style" issues and issues
in molfile sourcecode.

I fixed changlog CHANGES/v2.0.txt since it was not properly
showing (probably doxygen 1.8.6 could interpret it correctly)

[makedoc]

To have the noisy behavior just compile with
make VERBOSE=1