(cherry picked from commit 2c272e4a)

(cherry picked from commit e1d01e84)

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

(cherry picked from commit 7152d46f)

Conflicts:
	patches/patch.sh

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

(cherry picked from commit a273bb84)

I removed one page (WhatsNew) and merged it in the changelog page for
2.0

Plumed paper has now a volume and page

Plumed.inc and Plumed.cmake are now regenerated each time.

(cherry picked from commit cff67707)

important changes should go first I think

Fixes #55

Fixes #53

Now give a warning in metadynamics if grid is adjusted to fit periodicity

Target shared library is deleted before attempting its creation.
In this manner, if an error arises during compilation, the
library will not be there.

It is important to have LOAD FILE=xxx.cpp working properly.
E.g. if there is an error during compilation, a possibly existing
library is deleted.

Now crashed when wrong keywords are used in COORDINATION SWITCH=...

when a domain of domain decomposition is empty.

The fix to #39 was incorrect since adding an int to a string
does not print it.

I also removed the redundant check that index is positive (it is unsigned)

Check for NULL pointers is postponed to class Atoms and is done only if
there are local atoms. This fixes the case where GROMACS put zero atoms in
 a processor and assign a NULL pointer to positions

doesn't have this keyword

(cherry picked from commit 57c32f90)

I removed an assert and added an if then plumed_merror

close #39

I fixed the usage of stopflag in driver so that it is clearer
that the program stops at the end of the present step and not
at the beginning of the following. This is obviously equivalent,
but shows that scope of the flag can be reduced to be defined
at the inner of the MD loop.

Even if this is not a bux fix, I consider it as paired with fix #47
and I merge it to v2.0