Toolkit2: Make subprocess invocation of ExaHyPE main code optional

Some people might not like the idea that the ExaHyPE code calls the Toolkit in order to (pre)parse specification files.

We should offer a specfile option within the specfiles to allow to generate code which does not calls a subprocess but instead expects the input to be JSON.

This could be seen as advance hotfix when people report problems in complex MPI environments.