Agent mode ignores pnpm's `modulesDir`: on pnpm 10.12+ every installed package is "not installed", and apply exits 0 leaving it unpatched

[mikolalysenko]

[agent] Found by the scheduled pnpm bug-hunt routine (ledger #303).

Summary

pnpm's modulesDir setting (modules-dir in .npmrc, modulesDir: in pnpm-workspace.yaml) renames the project's node_modules. Since pnpm 10.12.0, the default virtual store follows it (<modulesDir>/.pnpm), so a project with modulesDir: deps has no node_modules at all. Every package lives in deps/.pnpm/<name>@<ver>/node_modules/<name>.

The npm crawler only collects directories literally named node_modules, plus the configured roots in configured_install_roots (yarn classic --modules-folder from #493, and Rush common/temp from #518). It never reads pnpm's modulesDir. So agent-mode apply / scan --apply sees nothing installed. Because pnpm-lock.yaml resolves the purl, it classifies the installed package as lockfile-only (package_not_installed, "resolved by the project lockfile"), which by contract never fails the run. Result: exit 0, status success, and the installed copy stays unpatched.

Release 4.0.0 failed loudly on the same fixture (exit 1, "no matching packages were found on disk"). The v5 lockfile-only classification turned this into a silent pass.

Impact

• A pnpm 10.12+ / 11 / 12 project using modulesDir gets no agent-mode patches at all, and CI sees a green socket-patch apply.
• Agent vex stays honest (no_applicable_patches, exit 1), so there's no false attestation in agent mode. Hosted vex with modulesDir is untested here; Agent mode ignores yarn classic's --modules-folder: packages installed there are reported "not installed" and scan --mode agent exits 0 leaving them unpatched #493 saw the hosted false-attestation variant with yarn classic's modules folder.

Repro (pnpm 12.8.1, Linux, main 045d7ec)

mkdir proj && cd proj
echo '{"name":"root","version":"1.0.0","dependencies":{"is-odd":"3.0.1","left-pad":"1.3.0"}}' > package.json
printf 'modulesDir: deps\n' > pnpm-workspace.yaml          # pnpm 10: echo modules-dir=deps > .npmrc
pnpm install
ls deps/.pnpm                                               # is-number@6.0.0 is-odd@3.0.1 left-pad@1.3.0 lock.yaml
# .socket/manifest.json + blobs: a patch for pkg:npm/left-pad@1.3.0 package/index.js (prepends a marker)
socket-patch apply --offline
#   Note: 1 manifest patch targets a package not installed on this host (resolved by the project lockfile; skipped):
#     - pkg:npm/left-pad@1.3.0
#   Summary: 0 of 1 targeted patch applied, 0 already patched, 1 not found on disk
echo $?                                                     # 0
head -c 30 deps/.pnpm/left-pad@1.3.0/node_modules/left-pad/index.js   # upstream bytes, no marker
NODE_PATH=deps node -e 'require("left-pad")'                # loads the unpatched copy
socket-patch vex --offline --json --output v.json           # exit 1, no_applicable_patches (honest)

It's the same in a workspace (packages: [packages/*] + modulesDir: deps, with a member depending on left-pad): 0 of 1 applied, exit 0.

Expected vs actual

• Expected: agent mode patches the copy pnpm actually installed, as it already does for pnpm's virtualStoreDir (Fix npm crawler missing relocated dependency stores (#359, #362) #365), yarn classic's --modules-folder (Agent mode ignores yarn classic's --modules-folder: packages installed there are reported "not installed" and scan --mode agent exits 0 leaving them unpatched #493) and Rush's common/temp (npm crawler never looks in Rush's common/temp store: hosted vex attests a transitive dep not_affected while its installed copy is unpatched, and agent apply reports it package_not_installed #518). At minimum, an installed-but-unseen package must not be reported as lockfile-only. CLI_CONTRACT.md:1136 reserves the never-fails package_not_installed skip for a purl the lock resolves with no installed copy ("a platform-gated optional dependency, a devDependency under --omit=dev").
• Actual: success, exit 0, nothing patched.

Matrix (Linux, Node 22, main 045d7ec; each cell run 2×)

pnpm	modulesDir honoured where	virtual store	agent apply
7.33.7 / 8.15.9 / 9.15.9	.npmrc modules-dir=deps	node_modules/.pnpm (deps/ holds only links into it)	pass (store copy patched)
10.0.0 / 10.5.2 / 10.7.1 / 10.9.0 / 10.10.0 / 10.11.1	.npmrc	node_modules/.pnpm	pass
10.12.0 / 10.12.1 / 10.20.0 / 10.28.0 / 10.34.5	.npmrc	deps/.pnpm	fail: package_not_installed, exit 0
11.28.3 / 12.8.1	pnpm-workspace.yaml	deps/.pnpm	fail: same

First pnpm version affected: 10.12.0 (the virtual store moved under modulesDir). socket-patch release 4.0.0 on pnpm 12.8.1: exit 1, loud "no matching packages were found on disk". Main is silent (exit 0). macOS and Windows weren't probed (the routine's probe branches are on hold), but the cause is platform-independent.

Suspect code

• crates/socket-patch-core/src/crawlers/npm_crawler.rs:45 configured_install_roots handles .yarnrc --modules-folder and rush.json but not pnpm modulesDir (from pnpm-workspace.yaml on 10+ and .npmrc modules-dir on ≤10, plus pnpm's global config.yaml / rc).
• The lockfile-only classification behind the package_not_installed detail ("resolved by the project lockfile") is what turns the miss into exit 0.

No duplicate found: #362 covers virtualStoreDir, #493 covers yarn classic --modules-folder (closed via #520, yarn only), and #373 / #495 / #359 cover other stores.

[mikolalysenko]

[agent] Triage: p1 (pnpm). Confirmed on main 045d7ec: configured_install_roots (crates/socket-patch-core/src/crawlers/npm_crawler.rs:45) knows yarn classic's --modules-folder and Rush's common/temp, but nothing reads pnpm's modulesDir / modules-dir, and the workspace walk only collects dirs literally named node_modules. Not a duplicate of #362: that issue's remaining half is the global virtual store outside the project, which is a different location and a different decision (patch/shared_store.rs). No open PR touches this.

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[mikolalysenko]

[agent] Shares root cause with #696: configured_install_roots (crates/socket-patch-core/src/crawlers/npm_crawler.rs:45) knows yarn's --modules-folder and Rush's common/temp, but not pnpm's modulesDir / modules-dir, so the pnpm 10.12+ <modulesDir>/.pnpm store is never crawled. Will be fixed together.

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[mikolalysenko]

[agent] Claiming this issue (with #696; shared root cause: npm crawler never reads pnpm modulesDir, so the <modulesDir>/.pnpm store is not crawled). Branch: agent/fix-pnpm-modules-dir-crawl. Claim-ID: 2026-10-03T13:21:08Z-d5f086

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Generated by Claude Code

[mikolalysenko]

[agent] Draft PR: #698

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