Fix VEX attesting beside an unpatched same-lock copy (#935, #938, #939)

[Mikola Lysenko (mikolalysenko)]

LLM Description written by Claude Code:claude-opus-5-5

Fixes #938
Refs #935
Refs #939

Summary

A lockfile-only vex attested a package as not_affected even though the same lock also installed an unpatched copy of that exact name@version:

• pnpm (pnpm VEX attests not_affected while a file: directory or file: tarball copy of the patched package@version in the same pnpm-lock.yaml installs unpatched, and hosted/vendored scans give no warning for that copy #935): a file: directory or file: tarball copy beside the Socket-wired registry entry.
• yarn classic (Yarn classic VEX attests not_affected when yarn.lock also has a registry block for the patched name@version (e.g. after yarn add -W <pkg> --exact), though yarn installs only the unpatched registry copy #938): a registry block of the same version beside the Socket block, e.g. after yarn add -W left-pad --exact. yarn 1 installs one copy per name@version, from whichever block it resolves first.
• yarn berry (Yarn berry hosted and vendored scans miss a file:/URL copy of the patched package locked under another dependency name, so lockfile VEX (and vendored VEX after install) attests not_affected while that copy installs unpatched #939): a file: / url copy locked under another dependency name (lp2@file:…). The resolutions pin never reaches it.

Root cause (shared)

VEX discovery had no shared same-lock rule. contest_across_locks (vex/discover/mod.rs) skips evidence from the ref's own lock (e.file != r.source_file), so each extractor wrote its own same-lock check. Only npm (push_uncontested unwired) and yarn classic git copies had one.

Change

• Discovery::unpatched_copy + contest_within_locks (vex/discover/mod.rs): one same-lock rule every extractor shares. An extractor records a copy, and every ref of the same name@version in that lock is dropped with patched_ref_unattributable. The diagnostic names the copy's lock entry and how it installs. The copy also counts as resolved_elsewhere evidence for the cross-lock contest. It runs before contest_across_locks.
• yarn classic: a non-Socket tarball block becomes a copy (Yarn classic VEX attests not_affected when yarn.lock also has a registry block for the patched name@version (e.g. after yarn add -W <pkg> --exact), though yarn installs only the unpatched registry copy #938). The git-copy post-filter (Hosted and vendored yarn classic modes rewire git-sourced yarn.lock entries, so every later yarn install fails while scan and VEX report success #363) now goes through the shared rule instead of its own loop.
• pnpm: file: directory / tarball entries (v9 name@file: keys and legacy file: keys) become copies (pnpm VEX attests not_affected while a file: directory or file: tarball copy of the patched package@version in the same pnpm-lock.yaml installs unpatched, and hosted/vendored scans give no warning for that copy #935). Name and version come from the key and the name: / version: fields, falling back to the directory's or tarball's package.json. A directory holding another version is not a copy.
• yarn berry: a non-Socket file: / url locator becomes a copy of the package it really holds (Yarn berry hosted and vendored scans miss a file:/URL copy of the patched package locked under another dependency name, so lockfile VEX (and vendored VEX after install) attests not_affected while that copy installs unpatched #939). The name is read from the file: tarball's package.json, the file: directory's package.json (path resolved against the locator= workspace), or the registry tarball url path (…/<name>/-/<name>-<version>.tgz). A copy whose package can't be read is left alone.
• The vendored post-install vex gaps in Yarn classic VEX attests not_affected when yarn.lock also has a registry block for the patched name@version (e.g. after yarn add -W <pkg> --exact), though yarn installs only the unpatched registry copy #938 / Yarn berry hosted and vendored scans miss a file:/URL copy of the patched package locked under another dependency name, so lockfile VEX (and vendored VEX after install) attests not_affected while that copy installs unpatched #939 close through the same path. Discovery still recognizes the uuid but emits no ref for it, so the vendor ledger's claim is dead (rule 11) and is not attested.
• Ports Route Gradle digests through utils::digest #878 (7eda8d8, cherry-pick of 659ac2c). main fails utils::digest::tests::production_digests_go_through_the_helpers (the coverage / test-release jobs), and Route Gradle digests through utils::digest #878 is the open fix. This becomes a no-op once Route Gradle digests through utils::digest #878 lands.

Why #935 and #939 are Refs, not Fixes

Both issues also ask the hosted / vendored scans to warn about the unreached copy. That is a separate gap in four rewriters (pnpm and berry, hosted and vendored), not this discovery boundary. This PR fixes the false VEX attestation for both. The scan warnings are left as a follow-up on those issues.

Test evidence

Regression tests, red with contest_within_locks disabled and green with it:

Issue	Test
#935	vex::discover::npm::tests::issue_935_same_lock_file_copy_contests_the_pnpm_ref: v9 dir, v9 tgz, legacy dir, plus controls (wiring alone; dir of another version)
#938	vex::discover::yarn::tests::issue_938_classic_registry_block_of_the_same_version_contests_the_ref: plus control (registry block of another version)
#939	vex::discover::yarn::tests::issue_939_berry_other_name_copy_contests_the_ref: file: tgz, file: dir, registry url, plus controls (wiring alone; file: copies holding another package)

The existing classic_git_pattern_copies_are_never_attested also went red with the shared pass disabled, which confirms git copies now go through it.

Local runs:

• cargo test -p socket-patch-core --all-features --lib: 5248 passed. 4 permission-based tests fail only because this sandbox runs as root (copy_tree symlinked root, vlt_heal unremovable lock, poetry / requirements write failure). They pass in CI on main's head. The 5th failure was the digest guard, fixed by the Route Gradle digests through utils::digest #878 port.
• cargo test -p socket-patch-cli --all-features --lib --test e2e_vex_lockfile --test e2e_vex_redirect --test e2e_vex_vendor --test e2e_vex --test covgap_commands_vex: all green (847 + 12 + 19 + 311 + 31 + 28).
• cargo clippy --workspace --all-features -- -D warnings: clean.
• VEX discovery golden (redirect-npm.json): regenerated. The only change is an additive unpatched_copies section on yarn classic fixtures. No ref or diagnostic changed.
• cargo fmt: touched files are formatted. main itself isn't cargo fmt --check clean (about 120 files), and CI doesn't run fmt.
• Scan bench: the first push regressed yarn-classic/hosted / rescan by 16–18% because of a quadratic per-insert dedup. 980b7b6 removes it. A local socket-patch-bench compare --filter yarn-classic against main then shows +1.4% [-10.4, +8.1] and -3.0% [-8.1, +3.3], both ≈.

The npm / PyPI / gem wrappers don't need changes: this is Rust-only discovery logic.

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https://claude.ai/code/session_01RpNijzXr9S3AZY6xHUDwVH

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Note

Medium Risk
Changes VEX discovery and attestation boundaries for npm-family locks; behavior is heavily tested but incorrect contest logic could wrongly omit or keep refs.

Overview
Stops false VEX attestation when a lockfile wires a package to Socket but also installs an unpatched copy of the same name@version in that same lock.

Discovery gains a shared unpatched_copy / contest_within_locks path: extractors record competing installs, then any matching ref in that file is dropped with patched_ref_unattributable (diagnostic names the lock entry and how it installs). That pass runs before the existing cross-lock contest. pnpm records file: directory/tarball entries (#935); yarn classic treats non-Socket registry/git blocks beside a Socket block as copies (#938); yarn berry resolves file:/URL deps keyed under another name via tarball/directory package.json or registry URL shape (#939). Goldens add an unpatched_copies section; regression tests cover #935–#939.

Separately, SHA-1/SHA-256 hex in Gradle cache, JVM jar patching, and Maven sidecars now go through utils::digest helpers (aligned with #878).

^{Reviewed by Cursor Bugbot for commit 980b7b6. Configure here.}

[Mikola Lysenko (mikolalysenko)]

BugBot review

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[Mikola Lysenko (mikolalysenko)]

[agent] native (windows-latest, 1.2.0) (Bun patch compatibility, run 37476785866) failed on one cell: 1.2.0 workspace vendored → refusalCodesExact. The other 48 cells passed. I think this is the patch API, not this PR, but I haven't confirmed it yet:

• the cell took ~15 s against ~1 s for its neighbours, and finished in the same second another cell got API request failed with status 504. That cell passed on the script's own retry.
• this PR only changes the npm / pnpm / yarn VEX discovery readers. The Bun reader (vex/discover/bun.rs) and the Bun vendored backend are untouched.
• the same workspace shape passed in hosted mode in this job, on every other Bun version on Windows, and on macOS.

The run is still in progress, so GitHub won't re-run the failed job yet (403 "already running"). I'll re-run it once when the run finishes. If it fails again, I'll pull captures/1.2.0-workspace-vendored/result.json from the job's results artifact and treat it as a real failure.

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Stale Bugbot comment from a previous run.

[Mikola Lysenko (mikolalysenko)]

Ready for review at 980b7b6.

• CI: 517/517 latest check runs green or skipped. The one red job, native (windows-latest, 1.2.0) in Bun patch compatibility, failed at the install step. It passed on a rerun of the same commit. The PR doesn't touch Bun code.
• Bugbot: reviewed 980b7b6 with no findings, and no review threads are unresolved.
• Mergeability: 0 commits behind main, no conflicts. It's waiting only on a required human review.
• For reviewers: the shared same-lock rule in vex/discover/mod.rs and how it's used in npm.rs and yarn.rs, plus the updated redirect-npm.json golden.

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[Mikola Lysenko (mikolalysenko)]

bugbot run

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