The HILLS file was appended even when not restarting.

Now the file containing the configuration options is a .cpp file.
This limits the effect of the change in the configuration to
a single object file and remove the need for BUILDAFTER variable
in Makefiles

Since the SetupMolInfo action is used by other ones, I left it
in core/. It is however registered in setup/, so that it can be excluded
disabling that module. Moreover, I added a method so as to remove
a friend statement in PlumedMain

To do this I needed a small fix on Atoms so as to
allow external actions to modify atom positions

Namespaces are used now in bias/colvar/function/cltools

The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent

I added a src/cltools/CLTool.h which can be directly included from sources
in the cltools directory

An output file was not set

Configuration files ending in ".local" will not be tracked
by git