Bun isolated linker: transitive packages under node_modules/.bun are "not installed" in agent mode, and scan --mode agent exits 0 with them unpatched #366

[agent] Found by the scheduled Bun bug-hunt routine (ledger #306).

Summary

With Bun's isolated linker, every package lives at node_modules/.bun/<name>@<version>/node_modules/<name>. The importer's node_modules only holds symlinks to its direct deps. Agent mode never looks inside node_modules/.bun, so a transitive dependency is treated as lockfile-only. scan --mode agent reports it skipped / package_not_installed, doesn't record it in the manifest, and exits 0 with status: "success". The installed copy stays unpatched.

The isolated linker is Bun's default for new workspaces from Bun 1.3.x on (configVersion: 1 locks). On a fresh Bun 1.3.14 or 1.4.2 workspace with no bunfig.toml, agent mode doesn't patch any transitive dependency. It's also opt-in for any project through [install] linker = "isolated".

This is the Bun twin of #359 (npm install-strategy=linked / .store) and #362 (pnpm custom virtual store). The code path is different: the .bun store directory.

Impact

• The vulnerable transitive copy stays on disk while scan --mode agent --json --yes exits 0 with success. The patch isn't even written to .socket/manifest.json, so a later apply or the postinstall hook never retries it.
• get <uuid> and apply on such a purl fail loudly (partial_failure, exit 1, package_not_installed), which is at least honest. The silent path is scan.
• VEX correctly omits the package (package_not_found), so there's no false attestation.

Repro (Linux, bun 1.4.2, main f6b7fb9)

mkdir iso && cd iso
printf '{"name":"app","version":"1.0.0","dependencies":{"mkdirp":"0.5.6","left-pad":"1.3.0"}}\n' > package.json
printf '[install]\nlinker = "isolated"\n' > bunfig.toml
bun install
ls node_modules/.bun            # left-pad@1.3.0  minimist@1.2.8  mkdirp@0.5.6  node_modules
# patch API mock serving free patches for left-pad@1.3.0 and minimist@1.2.8 (the probe below embeds one)
socket-patch scan --mode agent --json --yes --api-url http://127.0.0.1:18901 --org test-org --api-token fake
echo $?                          # 0
head -c 22 node_modules/.bun/minimist@1.2.8/node_modules/minimist/index.js   # unpatched

Envelope excerpt: "status": "success", "lockfileOnlyPackages": 1, apply.patches: left-pad added (the direct symlink works), minimist skipped package_not_installed. node -e 'require.resolve("minimist",{paths:[dirname(require.resolve("mkdirp"))]})' resolves to the .bun/minimist@1.2.8/... copy, so the package is installed and in use.

The default-linker workspace shape reproduces the same way with no bunfig: a root {"workspaces":["packages/*"]} plus packages/a depending on mkdirp@0.5.6, on bun 1.3.14 / 1.4.2.

Control: the same project with linker = "hoisted" patches both packages.

Expected vs actual

• Expected: CLI_CONTRACT.md "Deeply nested transitive dependencies are fully supported", which says apply "patches a package by PURL … regardless of how deep in the dependency tree it was installed". The crawler already walks pnpm's .pnpm, legacy .<registry> stores and vlt's .vlt store for exactly this transitive-only-home layout. pkg_managers.rs even documents that bun's isolated linker "populates node_modules/.bun/".
• Actual: .bun falls through to the generic hidden-entry skip, so its entries are never probed or crawled.

OS × version

Releases: it's the same on 4.0.0 and 3.3.0 (npm @socketsecurity/socket-patch), so it isn't a regression.

Suspect code

• crates/socket-patch-core/src/crawlers/npm_crawler.rs:1069: the nested-walk hidden-entry skip used by find_by_purls (apply / rollback / get). .pnpm, .vlt and legacy pnpm stores are special-cased just above it; .bun is not.
• crates/socket-patch-core/src/crawlers/npm_crawler.rs:1392: the same skip in the crawl_all walk (scan), which is why the package shows up only through the lockfile supplement (lockfileOnlyPackages).
• crates/socket-patch-core/src/crawlers/pkg_managers.rs:93: the detector knows about .bun/ but only uses it for classification.

Probe run (3 OS × bun 1.2.23 / 1.3.14 / 1.4.2, main built on each runner): https://github.com/SocketDev/socket-patch/actions/runs/36765789215