Lab #901: doctor extensions --repair should remove stale bundle entries for deleted source files

Description

swamp doctor extensions --repair leaves stale bundle entries on disk when the source files they were built from no longer exist. Manual deletion of the bundle directory is required to clean up.

Steps to Reproduce

Have a local extension loaded from extensions/models/ (e.g. proxmox_vm_extras.ts, proxmox_storage.ts)
Publish the extension to the registry and pull it via swamp extension pull
Delete the local source files from extensions/models/
Run swamp doctor extensions --repair

Observed Behavior

doctor extensions --repair reports all checks as passing but leaves the stale bundle directory (e.g. .swamp/bundles/e9c5c01e/) in place. The --repair output still lists the deleted source paths alongside the new pulled-extension paths:

"sourcePath": "/Users/dmc/projects/ai-infra/extensions/models/proxmox_storage.ts",
"bundlePath": "/Users/dmc/projects/ai-infra/.swamp/bundles/e9c5c01e/proxmox_storage.js",

Even though extensions/models/proxmox_storage.ts no longer exists on disk.

Expected Behavior

swamp doctor extensions --repair should detect bundle entries whose source files no longer exist and remove them automatically — the same way it handles other inconsistent state. A user who deletes local extension source files and runs --repair should end up with a clean state without needing to manually rm -rf .swamp/bundles/<hash>/.

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doctor extensions --repair should remove stale bundle entries for deleted source files

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Relationships

#901 doctor extensions --repair should remove stale bundle entries for deleted source files