CLI: on checkout, rename folders (rather than deleting)

When running workflows locally, users often save temporary or backup files in the workflows folder. If using the CLI with --cache-steps for example the CLI will dump state files for that workflow's last run. And it's quite intuitive that if you're testing a workflow, you want to save your input and output files in the workflow folder

When checking out (or pulling an update), if a workflow is renamed the CLI will delete and re-create that whole folder. This is super annoying if you've saved a bunch of input files in there

So we need the intelligence on checkout to:

• detect if a workflow was renamed between the projects (not sure actually how we do this!)
• If so, rename the workflow folder, rather than deleting it
• Try heuristics and fuzzy matching to track a rename
• Maybe prompt users if they'd like to rename or re-build workflows (allow disable for CI runs)

We may also need to respect this stuff on alias

Start at the CLI checkout and pull-update paths, then trace how workflow folders are currently removed and recreated when names change. Use the --cache-steps case to verify that user files and state survive a rename; done should cover rename detection, alias handling, and an optional prompt that can be disabled for CI.