Also patch *.inc.in file

plumed.h should be included before any other include

To make the layout more consistent, I made new files:
Config.inc
ConfigInstall.inc
that are generated with a script, whereas:
Config.cpp
ConfigInstall.cpp
are included in the repository.
In this manner all cpp files are included in the repository.

Fixed deprecated header

driver-float was not documented

[makedocs]

[makedoc]

[makedoc]

[makedoc]

[makedoc]

Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

fixed an error introduced in
e2f37a30

Fix namespace name crystallisation -> crystallization

Avoid using namespace std in header files.

The reason is that the cpp files including that .h file
will automatically use namespace std

Added missing namespaces

These are the files generated automatically with the cmd
dictionaries. I renamed them to inc which is a more standard
extension for include files.

Almost is not anymore supported in v2.3

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

[makedoc]

[makedocs]

[makedoc]

This fixed a bug I introduced in 35ed62dc

Namely, now all the directories containing regtests should be explicitly listed
in regtest/Makefile. The result of the bug was that not all regtests were run