I used cppcheck --enable=all.

Detected by cppcheck

operator= did not work correctly. I put an assertion to check it is not
actually used.

This avoids complains from make doc

Allow to better isolate the heavy part to be parallelized

When using IFile or OFile only, it is sufficient to include
one of the two header files.

It was causing several memory leaks

There was a problem if starting compilation in some directory.
Now also the links to other directories are generated recursively,
thus are by construction up to date for all the used modules.

Notice that config/ and wrapper/ are treated as special cases

Conflicts:
	src/PlumedFile.cpp
	src/bias/MetaD.cpp

Also, consistently:
PlumedIFile -> IFile
PlumedOFile -> OFile
PlumedFileBase -> FileBase

Class providing actions should have the same name as the input directive

I replaced all the "using namespace PLMD" statements with explicit
namespace PLMD{ …… }. This is more clear and simplify the syntax for
defining operators

It is better to avoid them as they will propagate to source which
include those .h files

Conflicts:
	src/function/FuncPathMSD.cpp
	src/generic/DumpDerivatives.cpp
	src/generic/DumpForces.cpp
	src/generic/DumpProjections.cpp

As this is a strange and not very well tested feature, I remove it
at least temporarily.