Gem crawler misses a Bundler 4 `bundle install --standalone` tree (`./bundle`), so agent `apply` patches the system copy and VEX attests `not_affected` while the app loads the unpatched standalone copy

[mikolalysenko]

[agent] Found by the scheduled Bundler (RubyGems) bug-hunt routine (ledger #316).

Summary

bundle install --standalone installs the bundle into ./bundle/ruby/<api>/gems/ and writes bundle/bundler/setup.rb, which hardcodes those load paths. Apps load it with require_relative "bundle/bundler/setup". This is the usual layout for Lambda functions and self-contained CLIs.

Bundler 2.x also records BUNDLE_PATH: "bundle" in .bundle/config, and the ruby crawler follows that. Bundler 4 no longer remembers CLI flags, so it writes no .bundle/config at all. The crawler's roots are only config path, $BUNDLE_PATH, vendor/bundle and the gem env homes, so on Bundler 4 it never sees ./bundle:

• If no other copy exists, apply reports package_not_installed ("Resolved by the project lockfile but not installed on this host (lockfile-only)"), but the gem is installed.
• If the same name-version is also in a gem env home (a common case: another project, or a global gem install), apply patches that copy and reports success. vex then attests not_affected ("Patched via Socket patch …"), while the app still loads the unpatched ./bundle copy.

Impact

False VEX attestation, and an unpatched runtime that reports applied. Every Bundler 4 standalone project is affected.

Repro (Linux, Ruby 3.3.6, Bundler 4.0.17, main 045d7ec; any marker patch works)

gem install rack -v 3.2.7            # an ambient copy of the same version
mkdir app && cd app
printf 'source "https://rubygems.org"\ngem "rack", "~> 3.1"\n' > Gemfile
bundle _4.0.17_ install --standalone  # -> ./bundle/ruby/3.3.0/gems/rack-3.2.7, no .bundle/config
# stage .socket/manifest.json + blob for pkg:gem/rack@3.2.7 (patch lib/rack.rb, append a probe constant)
socket-patch apply --json            # success, 1 applied
grep -c PROBE "$(gem env gemdir)/gems/rack-3.2.7/lib/rack.rb"   # 1  (system copy patched)
grep -c PROBE bundle/ruby/3.3.0/gems/rack-3.2.7/lib/rack.rb      # 0  (standalone copy untouched)
socket-patch vex --offline --product pkg:gem/app@1 -O vex.json  # not_affected / inline_mitigations_already_exist
ruby -e 'require_relative "bundle/bundler/setup"; require "rack"; p defined?(Rack::PROBE)'  # nil, loads ./bundle/.../rack.rb

If you skip the gem install line, apply skips with package_not_installed, and vex omits the purl (package_not_found).

Expected vs actual

• Expected: the crawler covers the install roots Bundler actually uses. ruby_crawler.rs documents probing "the bundler install roots, probed in bundler's own precedence order", and CLI_CONTRACT.md's VEX rules say an unpatched installed copy must never be attested. The ./bundle tree is what bundle/bundler/setup.rb loads.
• Actual: on Bundler 4 the standalone root is invisible. The ambient copy is patched and attested instead.

OS × version

OS	Ruby	Bundler	.bundle/config after --standalone	Standalone copy patched	VEX
Linux	3.3.6	2.4.22	BUNDLE_PATH: "bundle"	yes (pass)	correct
Linux	3.3.6	2.5.22	BUNDLE_PATH: "bundle"	yes (pass)	correct
Linux	3.3.6	2.6.9	BUNDLE_PATH: "bundle"	yes (pass)	correct
Linux	3.3.6	2.7.2	BUNDLE_PATH: "bundle"	yes (pass)	correct
Linux	3.3.6	4.0.17	none	no (×2 runs)	false not_affected

The crawler logic is OS-independent. The v4.0.0 release behaves the same way: it patches only the system copy. The trigger is Bundler 4 dropping remembered flags, not a socket-patch commit.

Suspect code

• crates/socket-patch-core/src/crawlers/ruby_crawler.rs:291-330 (discover_bundle_stores_with_env): the root list is config path → $BUNDLE_PATH → vendor/bundle, with no probe for a standalone bundle/ root (for example, one marked by bundle/bundler/setup.rb).
• ruby_crawler.rs:77-125 (gem_paths_and_discovery): because no project store is found, the gem env homes are appended, and those are what get patched and attested.

Hosted mode's stale-install guard probably misses the same root, because a re-run of bundle install --standalone would reuse the unpatched ./bundle copy. I haven't verified that; it's in the ledger backlog.

[mikolalysenko]

[agent] Triaged as priority:p1 (Bundler). I confirmed it on main 045d7ec: discover_bundle_stores_with_env (crates/socket-patch-core/src/crawlers/ruby_crawler.rs) only builds roots from the config path, $BUNDLE_PATH and vendor/bundle. Nothing probes a standalone ./bundle tree, for example one marked by bundle/bundler/setup.rb, so on Bundler 4, which writes no .bundle/config, the crawler falls back to the gem env homes. This is not a duplicate. #709 / PR #712 (an out-of-tree config path refused by the containment guard) is a different cause in the same function.

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[mikolalysenko]

[agent] Claiming this issue (shared root cause: the gem crawler's Bundler install-root discovery never probes a standalone ./bundle tree). Branch: agent/fix-gem-standalone-bundle-root. Claim-ID: 2026-10-04T17:21:06Z-743a63

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[mikolalysenko]

[agent] Draft PR: #797

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[mikolalysenko]

[agent] Re-triage from the Bundler bug-hunt routine (ledger #316): this still reproduces on main 045d7ec, and PR #797 (head 20898fd) fixes it. I used the same script for both builds: Bundler 4.0.17, bundle install --standalone, an ambient colorize 0.8.1 in GEM_HOME, then agent scan, then vex --offline.

Build	System copy patched	./bundle copy patched	VEX	require_relative "bundle/bundler/setup" loads
main 045d7ec	yes	no	not_affected (false)	unpatched
PR #797 20898fd	yes	yes	not_affected	patched

I haven't checked the hosted stale-install guard on the #797 build yet. It's still in the ledger backlog.

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