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Reinstating code snippets in the Topology User Manual #885
For some reason, some of the code snippets are missing from the Topology_UserManual.pdf, so this PR reinstates the snippets. As an example, see page 4 in the Topology manual in master, where we after the first line in section 2.1.1, page 4, should have
describing how we make a layer, but it is not there.
I have also cleaned up some of the code so that they do not exceed the grey box surrounding the snippets.