CLI checkout: make sure that renamed and removed workflows and jobs are updated

[josephjclark]

When running checkout, if a workflow or step has been renamed it seems we leave the old files on-disk and just generate new ones, creating a bit of a mess.

We need to be careful on checkout to recognise a rename and a delete and respond appropriately.

[josephjclark]

I think there are flavours of this in different issues: #1243 #1239