Implements the reorganisation of XIOS so that the contenxt is not closed...

Implements the reorganisation of XIOS so that the contenxt is not closed before all modules are initialized. This means that some variables cannot be outputed anymore in thermosoil and condveg. This commit also updates routing_reg so that it work with the new XIOS organisation. It also provides the new xml files needed. The standard xml files have not yet been updated.