Fixes for host network generation and probing Pass Nodes

* The host network was generated without flattening or removing pass nodes, this is corrected.  (Thanks for spotting this @neworderofjamie / @tcstewar)
* Custom build Nodes (those with a `spinnaker_build`) method were being disconnected from Nodes on the host.  These connections are now like Node->Ensemble/Ensemble->Node connections when connecting to non-custom build Nodes.
* The probes were being replaced rather than modified when removing the synapse attribute: this led to `KeyErrors` when trying to retrieve output values.