Lab #920: repo upgrade reports success but extension commands still warn about pending migration

Description

swamp extension rm warns that extensions are pending migration and tells the user to run swamp repo upgrade. Running swamp repo upgrade reports success, but the next extension command still shows the same pending-migration warning.

This makes it look like the upgrade command completed without actually clearing the migration state, or that the warning does not reflect what repo upgrade is able to fix.

Steps to reproduce

In a repository where extension commands warn about pending migration, run:
```
swamp extension rm @magistr/fc-agent-proxy
```

Observe the warning:

warning extension·rm         5 extension(s) pending migration. Run 'swamp repo upgrade' to complete.

Complete or cancel the extension removal prompt.
Run:
```
swamp repo upgrade
```

Observe output like:

info    extension·install    Reading lockfile...
info    extension·install    All extensions up to date.
info    repo·upgrade         Upgraded swamp repository: "20260630.112427.0" → "20260630.112427.0" (tools: "pi")
info    repo·upgrade           Changed files:
info    repo·upgrade             .swamp.yaml

Run another extension command, for example:

swamp extension rm @magistr/fc-task-server@2026.06.12.1

Expected behavior

After swamp repo upgrade reports success, extension commands should no longer warn that extensions are pending migration. If migration cannot be completed, repo upgrade should report an actionable reason and identify what remains pending.

Actual behavior

The same warning is shown again:

warning extension·rm         5 extension(s) pending migration. Run 'swamp repo upgrade' to complete.

Environment

Current swamp version: 20260630.112427.0-sha.0e5078e9
swamp update --check --json reports latest available: 20260702.205250.0-sha.1ba549d7
The issue was observed on the current installed version above; I did not verify whether the latest available version changes this behavior.

Fix scope

This affects repository upgrade / extension migration state handling. The fix would likely involve making repo upgrade reconcile the pending-extension migration marker/state that extension commands check, or making the extension-command warning point to the correct recovery action when repo upgrade cannot clear it.

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Relationships

#920 repo upgrade reports success but extension commands still warn about pending migration