Fix npm VEX attesting packages with an unpatched bundled copy (#325) (#337)

* Start fix for #325

Assisted-by: Claude Code:claude-opus-5-5

* Don't attest npm patches a bundled copy bypasses

A project can install the same name@version twice: the lock entry the
hosted or vendored rewriter points at Socket's patched tarball, and a
copy bundled inside another package (inBundle / bundled). npm unpacks
the bundled copy from its parent's tarball, so it stays unpatched, and
the rewriters already warn about that. VEX still attested the package
not_affected, because lockfile discovery skipped bundled entries
entirely.

Discovery now records each bundled entry's name@version. A Socket
reference with a bundled copy of the same version in either npm lock
is reported as patched_ref_unattributable, naming the bundled
location, and is not attested. The bundled copy also contests the
same package in other lockfiles. This covers the in-run scan --vex,
lock-basis and post-install vex runs in hosted and vendored mode.

Fixes #325

Assisted-by: Claude Code:claude-opus-5-5

* Document the bundled npm copy VEX contest

Adds the CHANGELOG entry and the CLI contract rule: a bundled npm
copy of a patched name@version keeps that patch from being attested.

Refs #325

Assisted-by: Claude Code:claude-opus-5-5

---------

Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: Mikola Lysenko <mik@socket.dev>

Author: 3 people

CHANGELOG.md

@@ -129,6 +129,11 @@ limits, and required install commands.
   not build from a previous patch's modified bytes. Verified service artifacts
   keep their identity; integrity failures do not fall through to a local rebuild.
   Repair rebuilds against recorded pins and reports unavailable inputs.
+- VEX no longer attests an npm package that also ships a bundled, unpatched
+  copy of the same `name@version` (`inBundle: true`, or v1 `bundled: true`).
+  npm unpacks that copy from the parent's tarball, so no rewire reaches it; the
+  reference is now reported `patched_ref_unattributable`, naming the bundled
+  copy, in hosted and vendored mode (#325).
 - API throttling uses bounded retries, failed queries appear in JSON diagnostics,
   and hosted reference resolution handles batches larger than 500 patches.
 - Transient apply locks are removed on normal command exit; no-op scans and full

crates/socket-patch-cli/CLI_CONTRACT.md

@@ -374,7 +374,7 @@ Recognition rules that hold for every ecosystem:
 
 * **Patch hosts.** A hosted reference counts only on `https://patch.socket.dev` or the `--patch-server-url` / `SOCKET_PATCH_SERVER_URL` origin, with no userinfo. The uuid is the URL's LAST canonical-uuid path segment, because grant tokens may themselves be uuid-shaped. The Go module prefix is fixed. `socket-patch-<uuid>` registry / repository / source names count only through a pin. For a URL on any other host, see **Patch hosts** above.
 * **Pins, not definitions.** A registry, index or source *definition* alone (cargo `[registries]`, nuget `<add>`, pom `<repository>`, uv index tables, `.npmrc`) never makes a reference, because it survives a reverted pin. Sections the package manager ignores are not read: npm's v2 `dependencies` mirror, a `.cargo/config.toml` shadowed by `.cargo/config`. A Socket pin inside a maven `<profile>` is diagnosed, never a reference.
-* **Contested locks.** When one lock wires a package to a patch and another lock resolves the same `name@version` from a non-Socket source, the build's bytes depend on which package manager runs. The reference is then dropped with a `patched_ref_unattributable` diagnostic naming both files. This applies across npm / pnpm / yarn / bun and across uv / pylock / poetry / pdm / Pipfile.lock / requirements. PEP 723 script locks neither contest nor are contested.
+* **Contested locks.** When one lock wires a package to a patch and another lock resolves the same `name@version` from a non-Socket source, the build's bytes depend on which package manager runs. The reference is then dropped with a `patched_ref_unattributable` diagnostic naming both files. This applies across npm / pnpm / yarn / bun and across uv / pylock / poetry / pdm / Pipfile.lock / requirements. PEP 723 script locks neither contest nor are contested. A **bundled** npm copy (`inBundle: true`, or v1 `bundled: true`) of the same `name@version` contests the reference too, in the same lock, in the other npm lock of a shrinkwrap/package-lock pair, or in any other lock. npm unpacks it from the parent package's tarball, so no rewire reaches it and it stays unpatched.
 * **Lockless pins.** With no lock to name a version, a `Cargo.toml` pin (every declaration on `socket-patch-<uuid>`, that registry defined on the patch host for the same uuid) or an exclusive nuget exact-id mapping is never a reference on its own, so v5.0 does not attest it (nor does `list` show it, or `rollback` / `remove` restore it — restore those files from version control). Only a pre-v5 redirect-ledger record naming a version the pin admits keeps it live. The same holds for a gem wired only in the `Gemfile` (the pre-bundler-2.6 mixed state, lock not converged).
 
 **Record resolution.** A candidate's record must carry the patch uuid the lockfile actually **wires**. It is taken from the first source that has one: the manifest (matched qualifier-insensitively), the hosted records above (this run's, then a pre-v5 ledger's), then the vendor ledger's embedded records. If none has it and the run is online, `vex` fetches the patch view by uuid from the patch API — for a v5 hosted checkout this is the normal path. The fetch uses `get`'s API client: the public proxy when no token is configured, and a one-shot 401/403 fallback to the proxy (free patches only). At most 10 fetches run concurrently. Fetched records stay in memory: `vex` never writes the manifest. A candidate still has no record under `--offline`, after a transport error or a 404, or when the patch is refused (paid without an entitled token); it is then omitted as `record_unavailable`, and the run is not aborted. A record whose uuid or package disagrees with the wiring is omitted as `record_mismatch`. The informational `socket-patch.vendor.json` marker is never a record source. When the lockfile wires a package to patch U, a manifest or ledger record for that package under another uuid is superseded, and a human-mode `Note:` says so.

crates/socket-patch-cli/tests/e2e_vex_redirect.rs

@@ -1618,6 +1618,61 @@ fn a_sibling_lock_resolving_the_registry_contests_a_ledger_record() {
     }
 }
 
+/// REGRESSION (#325): the hosted rewriter rewires the hoisted
+/// `left-pad@1.3.0` and skips a parent's bundled copy of the same version
+/// (`redirect_npm_bundled_instance_skipped`: npm unpacks it from the
+/// parent's tarball, so it stays unpatched). The ledger record must be dead
+/// (`redirect_unwired`, naming the bundled copy), not attested from the
+/// lock basis. Without the bundled copy the same ledger attests.
+#[test]
+fn hosted_npm_patch_with_an_unpatched_bundled_copy_is_not_attested() {
+    let purl = "pkg:npm/left-pad@1.3.0";
+    for bundled in [false, true] {
+        let tmp = tempfile::tempdir().unwrap();
+        let cwd = tmp.path();
+        write_hosted_package_lock(cwd, &[("left-pad", "1.3.0", UUID)], true);
+        if bundled {
+            let lock_path = cwd.join("package-lock.json");
+            let mut lock: Value =
+                serde_json::from_str(&std::fs::read_to_string(&lock_path).unwrap()).unwrap();
+            let packages = lock["packages"].as_object_mut().unwrap();
+            packages.insert(
+                "node_modules/bund".to_string(),
+                serde_json::json!({ "version": "1.0.0", "resolved": "file:bund-1.0.0.tgz" }),
+            );
+            packages.insert(
+                "node_modules/bund/node_modules/left-pad".to_string(),
+                serde_json::json!({
+                    "version": "1.3.0",
+                    "resolved": "https://registry.npmjs.org/left-pad/-/left-pad-1.3.0.tgz",
+                    "inBundle": true
+                }),
+            );
+            std::fs::write(&lock_path, lock.to_string()).unwrap();
+        }
+        write_redirect_ledger(
+            cwd,
+            &[(
+                purl,
+                make_record(UUID, &"b".repeat(64), "GHSA-bndl-host", &["CVE-2026-325"]),
+            )],
+            &[("package-lock.json", "npm_lock_entry")],
+        );
+        let (code, env) = vex_json(cwd, &["--offline", "--no-verify"]);
+        if !bundled {
+            assert_eq!(code, Some(0), "control: {env}");
+            continue;
+        }
+        assert_eq!(code, Some(1), "{env}");
+        assert_eq!(skipped_reason(&env, purl), "redirect_unwired", "{env}");
+        assert!(
+            env.to_string()
+                .contains("node_modules/bund/node_modules/left-pad"),
+            "the bundled copy is named: {env}"
+        );
+    }
+}
+
 /// REGRESSION: a hosted pin with NO lock at all is the rewriters' ordinary
 /// output, not a stale shape — `rewrite_nuget` edits only nuget.config for a
 /// project without RestorePackagesWithLockFile, `rewrite_cargo` only

crates/socket-patch-cli/tests/e2e_vex_vendor.rs

@@ -1343,6 +1343,135 @@ fn vendored_live_tree_out_of_sync_warns_but_attests() {
     );
 }
 
+/// REGRESSION (#325): the lock rewires the hoisted `lodash@4.17.21` to the
+/// vendored tarball, but a parent package also BUNDLES `lodash@4.17.21`
+/// (`inBundle: true`). npm unpacks that copy from the parent's tarball, so
+/// no rewire reaches it and the build ships it unpatched. `vex` must not
+/// attest the purl, from the lock basis (no `node_modules`) or after an
+/// install whose hoisted copy is patched and bundled copy is not. The
+/// same lock without the bundled copy is the control and still attests.
+#[test]
+fn vendored_npm_patch_with_an_unpatched_bundled_copy_is_not_attested() {
+    let purl = "pkg:npm/lodash@4.17.21";
+    let uuid = "0a0a0a0a-1111-4111-8111-0a0a0a0a0a0a";
+    let patched = b"patched npm bytes\n";
+    let after_hash = compute_git_sha256_from_bytes(patched);
+    for (label, bundled, installed) in [
+        ("control, lock basis", false, false),
+        ("bundled, lock basis", true, false),
+        ("bundled, installed", true, true),
+    ] {
+        let tmp = tempfile::tempdir().expect("create tempdir");
+        let cwd = tmp.path();
+        let rel = format!(".socket/vendor/npm/{uuid}/lodash-4.17.21.tgz");
+        let sha256 = sha256_hex(&write_member_tgz(
+            &cwd.join(&rel),
+            "package/index.js",
+            patched,
+        ));
+        let record = make_record(
+            uuid,
+            "package/index.js",
+            &after_hash,
+            "GHSA-bndl-aaaa",
+            &["CVE-2026-325"],
+        );
+        let wiring = write_matrix_wiring(cwd, "npm", uuid, &rel);
+        if bundled {
+            let lock_path = cwd.join("package-lock.json");
+            let mut lock: Value =
+                serde_json::from_str(&std::fs::read_to_string(&lock_path).unwrap()).unwrap();
+            let packages = lock["packages"].as_object_mut().unwrap();
+            packages.insert(
+                "node_modules/bund".to_string(),
+                serde_json::json!({ "version": "1.0.0", "resolved": "file:bund-1.0.0.tgz" }),
+            );
+            packages.insert(
+                "node_modules/bund/node_modules/lodash".to_string(),
+                serde_json::json!({
+                    "version": "4.17.21",
+                    "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
+                    "integrity": "sha512-T1JJR0lOQUw=",
+                    "inBundle": true
+                }),
+            );
+            std::fs::write(&lock_path, lock.to_string()).unwrap();
+        }
+        let mut state = VendorState::new();
+        state.entries.insert(
+            purl.to_string(),
+            detached_matrix_entry("npm", purl, uuid, &rel, sha256, record, wiring),
+        );
+        let dir = cwd.join(".socket/vendor");
+        std::fs::create_dir_all(&dir).unwrap();
+        std::fs::write(
+            dir.join("state.json"),
+            serde_json::to_string_pretty(&state).unwrap(),
+        )
+        .unwrap();
+        if installed {
+            for (pkg_dir, bytes) in [
+                ("node_modules/lodash", &patched[..]),
+                (
+                    "node_modules/bund/node_modules/lodash",
+                    b"original unpatched bytes\n",
+                ),
+            ] {
+                let nm = cwd.join(pkg_dir);
+                std::fs::create_dir_all(&nm).unwrap();
+                std::fs::write(
+                    nm.join("package.json"),
+                    r#"{"name":"lodash","version":"4.17.21"}"#,
+                )
+                .unwrap();
+                std::fs::write(nm.join("index.js"), bytes).unwrap();
+            }
+        }
+
+        let vex_path = cwd.join("out.vex.json");
+        let out = cli()
+            .args([
+                "vex",
+                "--cwd",
+                cwd.to_str().unwrap(),
+                "--json",
+                "--output",
+                vex_path.to_str().unwrap(),
+                "--product",
+                "pkg:npm/app@1.0.0",
+            ])
+            .output()
+            .expect("invoke vex");
+        let env: Value = serde_json::from_slice(&out.stdout).unwrap_or_else(|e| {
+            panic!(
+                "{label}: envelope JSON on stdout ({e}): {}",
+                String::from_utf8_lossy(&out.stdout)
+            )
+        });
+        if !bundled {
+            assert!(out.status.success(), "{label}: {env}");
+            let doc: Value =
+                serde_json::from_str(&std::fs::read_to_string(&vex_path).unwrap()).unwrap();
+            assert_eq!(
+                doc["statements"].as_array().unwrap().len(),
+                1,
+                "{label}: {doc}"
+            );
+            continue;
+        }
+        assert_eq!(out.status.code(), Some(1), "{label}: {env}");
+        assert!(
+            !vex_path.exists(),
+            "{label}: no VEX document may attest the purl: {env}"
+        );
+        assert!(
+            env.to_string()
+                .contains("node_modules/bund/node_modules/lodash"),
+            "{label}: the envelope names the bundled copy: {env}"
+        );
+    }
+}
+
 // ──────────────────────────────────────────────────────────────────────
 // 8. an applied, byte-verified agent-mode patch attests whether or not its
 // ecosystem has an install hook (there is no setup-state filter).

crates/socket-patch-core/src/vendor/lock_inventory/mod.rs

@@ -70,7 +70,7 @@ pub(crate) mod vlt;
 pub(crate) mod wired;
 pub(crate) mod yarn;
 
-pub(crate) use self::npm::{npm_lock_nodes, NpmLockNode};
+pub(crate) use self::npm::{npm_lock_bundled_nodes, npm_lock_nodes, NpmLockNode};
 #[cfg(test)]
 pub(crate) use self::npm_family::inventory_npm_lock;
 pub(crate) use self::pypi::pipfile_lock_entries;

crates/socket-patch-core/src/vendor/lock_inventory/npm.rs

@@ -44,20 +44,55 @@ const MAX_LEGACY_NPM_DEPTH: usize = 64;
 ///   through nested `dependencies`, `bundled: true` entries skipped (their
 ///   nested trees are still walked).
 pub(crate) fn npm_lock_nodes(doc: &Value) -> Vec<NpmLockNode<'_>> {
+    walk_npm_lock(doc, Bundled::Skip)
+        .into_iter()
+        .map(|(_, node)| node)
+        .collect()
+}
+
+/// The BUNDLED entries of a parsed npm lock, each with where the lock puts
+/// it: `inBundle: true` in `packages` (lockfileVersion 2/3; the location is
+/// the `packages` key), `bundled: true` in the v1 `dependencies` tree (the
+/// location is the `>`-joined chain of dependency names). These are exactly
+/// the entries [`npm_lock_nodes`] skips for being bundled, read from the
+/// same tree npm reads. npm unpacks them from the parent package's own
+/// tarball, so a Socket rewire never reaches them: a bundled copy of a
+/// patched `name@version` stays unpatched in the install (the rewriters
+/// warn `*_bundled_instance_skipped`), and lockfile discovery
+/// (`vex::discover::npm`) weighs it against the rewired entries.
+pub(crate) fn npm_lock_bundled_nodes(doc: &Value) -> Vec<(String, NpmLockNode<'_>)> {
+    walk_npm_lock(doc, Bundled::Only)
+}
+
+/// Which side of the bundled split [`walk_npm_lock`] returns.
+#[derive(Clone, Copy, PartialEq, Eq)]
+enum Bundled {
+    Skip,
+    Only,
+}
+
+/// [`npm_lock_nodes`] / [`npm_lock_bundled_nodes`]: one walk, split on the
+/// bundled flag. Locations are built only for [`Bundled::Only`] (empty
+/// otherwise), so the common walk allocates nothing extra.
+fn walk_npm_lock(doc: &Value, bundled: Bundled) -> Vec<(String, NpmLockNode<'_>)> {
     let mut out = Vec::new();
     if let Some(packages) = doc.get("packages").and_then(Value::as_object) {
         for (key, node) in packages {
             let Some((_, key_name)) = key.rsplit_once("node_modules/") else {
                 continue;
             };
-            if npm_flag(node, "link") || npm_flag(node, "inBundle") {
+            if npm_flag(node, "link") || npm_flag(node, "inBundle") != (bundled == Bundled::Only) {
                 continue;
             }
             let name = node.get("name").and_then(Value::as_str).unwrap_or(key_name);
-            out.push(NpmLockNode::of(name, node));
+            let location = match bundled {
+                Bundled::Only => key.clone(),
+                Bundled::Skip => String::new(),
+            };
+            out.push((location, NpmLockNode::of(name, node)));
         }
     } else if let Some(deps) = doc.get("dependencies").and_then(Value::as_object) {
-        walk_npm_legacy_dependencies(deps, 0, &mut out);
+        walk_npm_legacy_dependencies(deps, 0, bundled, "", &mut out);
     }
     out
 }
@@ -89,17 +124,24 @@ fn npm_flag(node: &Value, key: &str) -> bool {
 fn walk_npm_legacy_dependencies<'a>(
     deps: &'a serde_json::Map<String, Value>,
     depth: usize,
-    out: &mut Vec<NpmLockNode<'a>>,
+    bundled: Bundled,
+    parent: &str,
+    out: &mut Vec<(String, NpmLockNode<'a>)>,
 ) {
     if depth > MAX_LEGACY_NPM_DEPTH {
         return;
     }
     for (name, node) in deps {
-        if !npm_flag(node, "bundled") {
-            out.push(NpmLockNode::of(name, node));
+        let location = match bundled {
+            Bundled::Only if parent.is_empty() => name.clone(),
+            Bundled::Only => format!("{parent} > {name}"),
+            Bundled::Skip => String::new(),
+        };
+        if npm_flag(node, "bundled") == (bundled == Bundled::Only) {
+            out.push((location.clone(), NpmLockNode::of(name, node)));
         }
         if let Some(nested) = node.get("dependencies").and_then(Value::as_object) {
-            walk_npm_legacy_dependencies(nested, depth + 1, out);
+            walk_npm_legacy_dependencies(nested, depth + 1, bundled, &location, out);
         }
     }
 }