This is a huge commit, applying indentation to the whole
code.

See #215

I added a script located in src that applies astyle to
all source files and add them to git. This script can
be invoked as `make astyle`.

File .astyle.options contains the astyle command line options

See #215

Prior to this change a misuse of the LOWMEM keyword could cause segfaults.
Now these cases crash with an error.

MOVINGRESTRAINT with TORSION

It is difficult to remove the main timer, but at least I
added a timer that makes sense

Fixes #194

[makedoc]

[makedoc]

- 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 reverts commit 37001778.

This reverts commit 8dab6d81.

(sorry)

It now detects if different replicas have different bias-factor

removed mention to a bug that is not actually there

This is a nasty workaround. Since FIT_TO_TEMPLATE needs to
access forces stored in Atoms, it is necessary that they are kept up
to date. With this fix, there is an extra function
allowToAccessGlobalForces()
that switch off an optimization that would otherwise make the
forces wrong when running in parallel

Set pointer to NULL with plumed_finalize() (to avoid subsequent usage)

addresses #213

[makedoc]

addresses #213

[makedoc]