ROVER-326 Ensure Rover expands references in the supergraph.yaml
#2411
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Fixes: #2408
Following the refactor we have introduced a regression where before variable references in the
supergraph.yaml
would be expanded and now they are not. This PR fixes that so that variables are expanded again.In addition some cleanup work had not happened after the refactor, leaving lots of code that was not being used. This resolves that too