Scan of a fresh Poetry checkout (no Poetry env yet, default virtualenvs.create) crawls the system Python: vendored exits 1 on system-only packages and agent mode patches dpkg-owned files (the Poetry side of #947 / #964) #1023

[agent] Found by the scheduled Poetry bug-hunt routine (ledger #311).

Summary

This is the Poetry counterpart of #947 (Pipenv, fixed by #950) and #964 (uv, open PR #965). Neither fix covers Poetry. #950 guards only is_pipenv_project, and #965's new uv_owns_project_env returns false for any [tool.poetry] / poetry.lock project through claimed_by_non_uv_manager.

Take a Poetry project checked out fresh: it has pyproject.toml and poetry.lock, but poetry install hasn't run, so there's no in-project .venv and no out-of-tree env under virtualenvs.path. PythonCrawler::get_site_packages_paths finds no env. is_python_project(cwd) is true, so the crawl falls back to get_global_python_site_packages(), and every package in the OS Python joins the candidate set (scannedPackages: 86 for a 1-package lock). With the default virtualenvs.create = true, Poetry never installs a project into that interpreter. The env Poetry will create is the only one the project can have.

• Vendored tries to vendor the system-only packages into poetry.lock and fails with pypi_poetry_lock_package_missing ("poetry.lock has no [[package]] entry for six; run poetry lock first"), partial_failure, exit 1. The remedy doesn't help, because six isn't a project dependency.
• Agent patches the system copy in place, for example the dpkg-owned /usr/lib/python3/dist-packages/six.py, and exits 0. The project hasn't installed anything yet.
• Hosted lists the system package as a project package and warns No poetry.lock entry for six@1.16.0, exit 0.

Impact

• CI breakage in the documented vendored flow. A fresh checkout is exactly where vendored mode runs. Debian/Ubuntu images and GitHub ubuntu-* runners ship a system Python with six, PyYAML, requests, urllib3, idna and more. Whenever Socket has a patch for any of them, every vendored scan of every Poetry project on that machine exits 1, including projects whose own dependencies have no patches.
• Agent mode writes outside the project, into the OS package manager's files. The project's later poetry install then gets the unpatched release, while the manifest records the patch as applied.
• System copies mask lock entries: lockfileOnlyPackages drops, and patch counts and the rollout budget include packages that aren't part of the project.

Repro (Linux, Debian/Ubuntu-style system Python with python3-six in /usr/lib/python3/dist-packages; a local mock patch API offers free patches for six@1.16.0 and typing-extensions@4.7.1)

mkdir app && cd app
cat > pyproject.toml <<'EOF'
[project]
name = "demo-fresh"
version = "0.1.0"
requires-python = ">=3.9"
dependencies = ["typing_extensions==4.7.1"]

[build-system]
requires = ["poetry-core>=2.0"]
build-backend = "poetry.core.masonry.api"
EOF
poetry lock                                   # Poetry 2.5.1; older Poetry creates the env here:
rm -rf "$(poetry config virtualenvs.path)"/demo-fresh-*   # simulate the lock-only checkout
env -u VIRTUAL_ENV socket-patch scan --mode vendored --ecosystems pypi --yes --json \
  --api-url $MOCK --api-token x --org test-org --patch-server-url $MOCK > out.json; echo "exit=$?"
# exit=1, status partial_failure, scannedPackages 86, lockfileOnlyPackages 1
# vendor.events: six failed pypi_poetry_lock_package_missing; typing-extensions vendored fine

env -u VIRTUAL_ENV socket-patch scan --mode agent --ecosystems pypi --yes ...   # exit 0
tail -c 18 /usr/lib/python3/dist-packages/six.py   # the patched bytes: the system copy was modified

Control: run poetry install --no-root first. The same vendored scan then crawls only the Poetry env (scannedPackages: 2, lockfileOnlyPackages: 0) and exits 0 with success.

Expected vs actual

• Expected: CLI_CONTRACT.md, "cwd-only (single project)", says the pypi crawler inspects the project rooted at --cwd (its manager's env, $VIRTUAL_ENV, .venv / venv). Global packages are the -g / --global-prefix surface. On a fresh checkout, lock-only packages already come from poetry.lock (lockfileOnlyPackages). With virtualenvs.create true (the default), the empty Poetry-env result should be final, just as Fix Pipenv project falling back to system Python (#504, #947) #950 made it for Pipenv. Vendored should vendor typing-extensions and exit 0. Agent should report it as not installed and touch nothing outside the project.
• Actual: system-Python packages join the candidate set. Vendored exits 1 with a misleading poetry lock remedy, and agent mode modifies the system interpreter's files.

virtualenvs.create = false is the one Poetry case where the current interpreter really is the project's env, so the fallback is legitimate there (verified: 86 scanned, as intended).

Cells (main db83f01, Linux x86_64, system Python 3.11 + Debian python3-six; each wet cell run twice)

Release 4.0.0 behaves the same (exit 1, partial_failure), so this isn't a recent regression. The fallback predates vendored Poetry support. macOS and Windows weren't probed (probe branches are blocked for this routine), but get_global_python_site_packages also scans Homebrew, python.org and conda roots, so the same fallback applies there.

Suspect code

• crates/socket-patch-core/src/crawlers/python_crawler.rs:3052-3058: after Fix Pipenv project falling back to system Python (#504, #947) #950, only is_pipenv_project short-circuits. is_python_project then sends a Poetry project to get_global_python_site_packages().
• crates/socket-patch-core/src/crawlers/python_crawler.rs:367-373: poetry_project_site_packages returning empty falls through to the generic .venv / venv probe and then to the global fallback. Poetry's config (virtualenvs.create) already says whether the system interpreter can be the env.
• PR Fix uv project with no env falling back to system Python (#964) #965 (claimed_by_non_uv_manager / uv_owns_project_env) leaves Poetry projects on the fallback path on purpose. A Poetry guard can reuse the same shape: when load_poetry_project succeeds and virtualenvs.create resolves true, an empty result is final.

Related: #947 / #950 (Pipenv), #964 / #965 (uv), #504 (agent-mode system writes, Pipenv), #476 / #527 (Poetry in-project = true with an existing out-of-tree env), #671 (create = false + stray venv).