use same tolerance in mesh extrusion as in geometry ; if this tol is too large, we should introduce another option

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Replaced MVertexPositionSet with MVertexRTree ; use MVertexRTree in all extrusion algorithms instead of the (incorrect) std::set<MVertex, MVertexLessThanLexicographic>

Introducing Dof::RejectedDof() to handle Dofs that are not part of FunctionSpace in both assembly and interpolation -- Seems ok