fix(arborist): re-apply packageExtensions to the linked actual tree (#9569)

Follow-up of #9496

Under `install-strategy=linked`, a root `packageExtensions` rule that
adds a missing dependency installs and works at runtime, but every
command that reads the actual tree loses the edge:

- `npm ls --all --json` omits the extension-created dependency and its
provenance.
- `npm explain <dep>` fails with `No dependencies found matching <dep>`.
- `npm patch add <dep>` fails with `EPATCHNOTINSTALLED`.

Hoisted installs and normally-declared transitive deps are unaffected.

## References

Fixes #9568