Lab: Per-extension layout migration drops Claude skill from @magistr/good-planning

Description

After running `swamp self-update` from `20260428.090310.0-sha.7bd1c276` to `20260501.150516.0-sha.acc85d5a`, the auto-migration to the new per-extension layout dropped the Claude skill that was provided by an already-pulled extension.

Migration log line observed:

``` Migrating "@magistr/good-planning"@"2026.05.01.1" to per-extension layout... ```

After the migration completed, the `good-planning` Claude skill was no longer registered/available. Running `swamp extension pull @magistr/good-planning` again restored the skill.

Steps to reproduce

On swamp `20260428.090310.0-sha.7bd1c276`, pull the extension: `swamp extension pull @magistr/good-planning` (version `2026.05.01.1`).
Confirm the `good-planning` Claude skill is registered and usable.
Run `swamp self-update` to `20260501.150516.0-sha.acc85d5a`.
Observe the migration message: `Migrating "@magistr/good-planning"@"2026.05.01.1" to per-extension layout...`.
Verify the Claude skill from the extension — it is now missing.
Re-run `swamp extension pull @magistr/good-planning` — skill returns.

Expected

The per-extension layout migration should preserve all extension-provided assets, including Claude skills, so a re-pull is not required.

Actual

Migration completes "successfully" but Claude skill is dropped. Only a fresh `swamp extension pull` reinstates it.

Environment

Pre-update swamp: `20260428.090310.0-sha.7bd1c276`
Post-update swamp: `20260501.150516.0-sha.acc85d5a`
Extension: `@magistr/[email protected]`
Platform: macOS (Darwin 23.6.0)

Workaround

Re-run `swamp extension pull @magistr/good-planning` after migration.

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