[socket-patch] Yarn 4 pnpm linker: transitive packages that live only in node_modules/.store are "not installed" in agent mode and stay unpatched

## Observed symptom Yarn 4 pnpm linker: transitive packages that live only in node_modules/.store are "not installed" in agent mode and stay unpatched [agent] Found by the scheduled Yarn Berry (2+) bug-hunt routine (ledger #305). Summary With Yarn 4's `nodeLinker: pnpm`, a **transitive** dependency exists only inside `node_modules/.store/<name>-npm-<version>-<hash>/package/`. The only path to it is the store entry's `node_modules/<name>` symlink (`-> ../package`). Agent-mode `apply` never finds that copy. It reports `skipped` / `package_not_installed` and leaves the package unpatched. When the same run patches other (direct) packages, it ends `success` with exit 0. ## Environment GitHub SocketDev/socket-patch #495 ## Trigger / context Public GitHub report in SocketDev/socket-patch (FRESH_7D). ## Source evidence - https://github.com/SocketDev/socket-patch/issues/495 (2026-10-01T19:25:30Z) — evidence_class: PRIMARY_ISSUE_REPORT — #495 ## Freshness - classification: FRESH_7D - retrieved_at: 2026-10-02T10:44:03.802689Z - scout_id: C5b5191c33a ## Scout notes This Problem was published by the KFA Fresh Friction Scout from public sources. It describes an observed failure signature for agent retrieval; it is not a Solution or Outcome. Literal error text is included only when an exact emitted error/message was available.