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

[mikolalysenko]

[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.

#359 was fixed on main by #365 (61cfb9b, "Find packages in npm .store and pnpm virtualStoreDir"), which now walks node_modules/.store. That fix covers npm's linked layout, where .store/<name>@<v>-<hash>/node_modules/<name> is a real directory. Yarn 4 uses the same .store name, but there the node_modules/<name> child is a symlink to the sibling package/ dir, so the store-entry probe rejects it.

Yarn 3.x's pnpm linker writes real dirs at .store/<slug>/node_modules/<name> and isn't affected.

Impact

Every transitive dependency of a Yarn 4 project on the pnpm linker is unpatchable in agent mode, and when other patches apply the run gives no failure signal (exit 0). The docs say this layout is supported:

• docs/ecosystems.md: "Inside each node_modules, the package stores of isolated layouts are walked too, since they are the only home of transitive dependencies: … npm's install-strategy=linked store node_modules/.store."
• docs/testing/yarn-berry-compatibility.md: the node-modules and pnpm linkers "are covered end to end". The pnpm-linker e2e (e2e_yarn4_pnpm_linker_build) only patches a direct dependency.

Repro (Linux, Node 22, yarn 4.12.0)

mkdir p && cd p
echo '{"name":"p","version":"1.0.0","dependencies":{"is-odd":"3.0.1","left-pad":"1.3.0"}}' > package.json
printf 'nodeLinker: pnpm\n' > .yarnrc.yml && touch yarn.lock
yarn install
ls -l node_modules/.store/is-number-npm-6.0.0-*/node_modules/   # is-number -> ../package
# Stage an agent-mode manifest (.socket/manifest.json + .socket/blobs) with two patches:
#   pkg:npm/is-number@6.0.0  (transitive, via is-odd) file package/index.js
#   pkg:npm/left-pad@1.3.0   (direct)                 file package/index.js
# (after blob = "/* SOCKET-PATCHED */\n" + original index.js; git-sha256 hashes)
SOCKET_NO_CONFIG=1 socket-patch apply --json; echo "exit=$?"
head -c 20 node_modules/.store/is-number-npm-6.0.0-*/package/index.js

Actual (main 61cfb9b):

status: success  summary: {"applied": 1, "skipped": 1, "failed": 0, …}
{"action":"applied","purl":"pkg:npm/left-pad@1.3.0","files":[{"path":"package/index.js","verified":true,"appliedVia":"blob"}]}
{"action":"skipped","purl":"pkg:npm/is-number@6.0.0","reason":"No installed package matches this PURL","errorCode":"package_not_installed"}
exit=0
/*!\n * is-number      <- unpatched

With only the is-number patch staged, the run is partialFailure / exit 1 with the same package_not_installed skip.

Expected vs actual

• Expected: the store copy at .store/is-number-npm-6.0.0-<hash>/package is found and patched, as the docs above promise for isolated-store transitive dependencies (and as already happens for npm's .store, pnpm's .pnpm and Yarn 3's pnpm linker).
• Actual: package_not_installed, file untouched, exit 0 when anything else applied.

OS × version

OS	yarn	linker	transitive dep in .store
Linux	3.8.7	pnpm	pass (real dir in the store entry)
Linux	4.0.2	pnpm	fail
Linux	4.12.0	pnpm	fail (reproduced twice, plus a scoped direct dep as control: patched)
Linux	4.18.1	pnpm	fail
Linux	4.12.0	node-modules	pass (control: hoisted node_modules/is-number patched)

macOS and Windows weren't probed. The layout is yarn's own (symlinks on POSIX, junctions on Windows), so they're likely affected the same way.

First bad version

Not a regression. Release 4.0.0 (npm @socketsecurity/socket-patch) behaves identically on the same tree. 61cfb9b didn't extend .store support to Yarn's layout.

Suspect code

• crates/socket-patch-core/src/crawlers/npm_crawler.rs:1140: in visit_resolver_dir, a store-entry node_modules rejects any target that isn't a real directory (is_real_package_dir_sync, npm_crawler.rs:2361, uses symlink_metadata(..).is_dir()). Yarn's node_modules/<name> -> ../package is a symlink to the entry's own package/ dir, which is the only physical copy. Nothing walks <entry>/package directly.
• list_npm_store_entries_sync / decode_npm_store_entry_name (npm_crawler.rs:231, ~1951) parse npm's <name>@<version>-<hash> key. Yarn's keys are <slug>-npm-<version>-<hash> (scoped: @scope-name-npm-…), so the advertised name/version is never decoded for them either.

No probe runs yet. macOS/Windows are on the routine's backlog.

[mikolalysenko]

[agent] Triaged: priority:p1 (Yarn Berry, npm family). Not a duplicate.

Shares root cause with #366, #373, #405: the npm crawler (crawlers/npm_crawler.rs) only recognizes isolated dependency stores by hard-coded names and shapes (.pnpm, .vlt, npm's .store with a real-dir node_modules/<name>). Bun's .bun and Deno's .deno fall into the generic hidden-entry skip, and Yarn 4's .store/<entry>/node_modules/<name> -> ../package link is rejected by the store-entry real-dir check. Will be fixed together.

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[mikolalysenko]

[agent] Claiming this issue (with #366, #373, #405; shared root cause: the npm crawler only recognizes isolated stores by hard-coded names/shapes, so .bun, .deno and Yarn 4's .store are skipped). Branch: agent/fix-npm-crawler-isolated-stores. Claim-ID: 2026-10-01T19:20:55Z-253dcb

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[mikolalysenko]

[agent] Draft fix PR: #496

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