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

Summary

On pnpm 10.5 and later, overrides: can live in pnpm-workspace.yaml. When a project keeps its overrides there, vendor (and scan / get --mode vendored) adds the vendored file: override to that block. It also creates a brand-new pnpm.overrides object in package.json, a back-compat copy kept for pnpm 9/10 since #174. On pnpm 10, a pnpm.overrides field in package.json replaces the workspace-file overrides instead of merging with them. So the effective override set becomes {[email protected]: file:…} alone, while the rewritten lock records the user's overrides plus ours.

vendor reports success and vex attests not_affected, but:

• every pnpm install --frozen-lockfile (CI, fresh clone, or the same checkout) fails with ERR_PNPM_LOCKFILE_CONFIG_MISMATCH.
• a plain pnpm install "fixes" this by re-locking without the user's overrides, which silently drops them. That can be a security pin, since overrides are commonly used for exactly that.

pnpm 11+ is unaffected, because it doesn't read the package.json pnpm field.

Repro (pnpm 10.34.5, Linux)

mkdir p && cd p
echo '{"name":"p","version":"0.0.0","private":true,"dependencies":{"left-pad":"1.3.0"}}' > package.json
printf "packages:\n  - '.'\noverrides:\n  is-number: 6.0.0\n" > pnpm-workspace.yaml
pnpm install                       # lock records overrides: {is-number: 6.0.0}
# stage a .socket/manifest.json + blobs for pkg:npm/[email protected] (hand-staged, as in tests/e2e_vendor_pnpm_build.rs)
socket-patch vendor --offline --json   # status: success, action: applied
cat package.json                   # NEW: "pnpm": {"overrides": {"[email protected]": "file:.socket/vendor/npm/<uuid>/left-pad-1.3.0.tgz"}}
cat pnpm-workspace.yaml            # overrides: is-number: 6.0.0 + [email protected]: file:…
# fresh checkout of the committable files, empty store:
pnpm install --frozen-lockfile --offline
#  ERR_PNPM_LOCKFILE_CONFIG_MISMATCH  Cannot proceed with the frozen installation. The current "overrides" configuration doesn't match the value found in the lockfile
socket-patch vex --offline --output v.json   # exit 0, not_affected
pnpm install --no-frozen-lockfile --offline
sed -n '/^overrides/,/^$/p' pnpm-lock.yaml
# overrides:
#   [email protected]: file:.socket/vendor/npm/<uuid>/left-pad-1.3.0.tgz      <- is-number: 6.0.0 is gone

Expected vs actual

• Expected: docs/ecosystems.md (vendored npm row) and fix(vendor): write pnpm overrides to pnpm-workspace.yaml for pnpm >= 11 #174 promise that the vendored lock plus overrides install with a cold pnpm install --frozen-lockfile --offline from the committable files, and that user overrides are preserved (a conflicting one is refused with vendor_override_conflict, per CLI_CONTRACT.md).
• Actual: vendoring succeeds, but the committable state can't be frozen-installed on pnpm 10.5+. The only remedy pnpm offers (a re-lock) deletes the user's overrides.

Matrix (Linux, current main f6b7fb9)

Released 4.0.0 behaves the same (not a v5 regression). This is config logic, not OS-specific.

Suspect code

crates/socket-patch-core/src/vendor/pnpm_lock.rs:1585 (apply_pkg_override) always creates pnpm.overrides in package.json. When pnpm-workspace.yaml already carries a top-level overrides: block (see ws_overrides_section, :1667, and apply_workspace_override, :1735), the package.json copy should be skipped, because on pnpm 10.5+ it shadows the workspace block. The alternative is to copy the user's workspace overrides into it, but that doubles the surface.