lake update does not update transitive dependency pins

When running lake update, direct dependencies are updated to their latest commits, but transitive dependencies are not re-resolved from the updated upstream package's manifest. This means stale transitive dependency pins can silently persist even after the direct dependency has been updated.

Reproduction

Given three projects:

• C (e.g. subverso) — a library
• B (e.g. verso) — depends on C via require C from git "..."@"main"
• A (e.g. reference-manual) — depends on B via require B from git "..."@"main"

1. A's lake-manifest.json has B pinned at commit b1 and C pinned at commit c1
2. B is updated: B's main now points to b2, and B's manifest pins C at c2
3. Run lake update in A

Expected: A's manifest updates B to b2 and C to c2 (from B's updated manifest)

Actual: A's manifest updates B to b2 but keeps C at c1

Concrete example

This happened during the v4.29.0-rc7 release with the reference-manual:

• subverso got a fix at 21e4badfe6a6 ("chore: prefer inferInstance, for v4.29.0-rc7")
• verso's main (7ad685cf1a9e) updated its manifest to pin the fixed subverso
• Running lake update in reference-manual updated verso to 7ad685cf1a9e but kept subverso at the old 699813355084, causing a build failure

The only workaround was to manually edit lake-manifest.json to update the subverso rev.

🤖 Prepared with Claude Code