I merge the patch --save-originals stuff on v2.0.
I am using it a lot and I think it is stable enough to go to v2.0.
This will allow to modify gromacs patch also in that version.

Conflicts:
	patches/patch.sh

(this file was removed)

I updated doxyfile to latest doxygen version. I also
enables the search engine. This required a small fix on the
extract script so that "action" pages receive a proper name
for the index.

I removed many graphs that were probably not useful
and were cluttering the output. Moreover, I
enabled the search engine and added an alphabetic
list of classes (classes -> class index)

Needed to have proper regeneration of links when new .h files are added.
I also added several comments.

Instead of using links to other source directories
we now use explicit include files. The approach is more
robust.

Closes #69

(thanks to Toni Giorgino)

I fixed a missing include.

Original comment:
Fixes in backup output files - cant rename open file under windows - print reason for failure - remove leak of FILE*s

(cherry picked from commit 448e84fc)

(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=...