[BUG-P2] test_auto_scans_on_fresh_workspace fails intermittently — clean_app fixture .codelens not gitignored

[Wolfvin]

Summary

tests/test_architecture.py::TestArchitectureBasic::test_auto_scans_on_fresh_workspace fails intermittently because benchmarks/fixtures/clean_app/.codelens/ is not gitignored. Tests that scan the clean_app fixture (e.g., test_vuln_staleness.py) create .codelens/osv_cache.db inside the fixture directory, which then pollutes the fresh_clean_app copy used by the architecture test.

Root cause

1. benchmarks/fixtures/clean_app/ is a fixture directory used by multiple tests.
2. Tests like test_vuln_staleness.py run vuln-scan on clean_app, which creates .codelens/osv_cache.db inside the fixture directory (not a temp copy).
3. test_auto_scans_on_fresh_workspace copies clean_app to a temp dir and asserts .codelens does NOT exist in the copy (because it's supposed to be a "fresh" workspace).
4. The copy includes .codelens (because it's now on disk), so the assertion fails.

Evidence

# Run test in isolation — still fails because .codelens is already on disk
PYTHONPATH=scripts python3 -m pytest tests/test_architecture.py::TestArchitectureBasic::test_auto_scans_on_fresh_workspace -v
# FAILED

# Check fixture directory
ls benchmarks/fixtures/clean_app/.codelens/
# osv_cache.db  ← created by previous test run, not gitignored

# Clean up
rm -rf benchmarks/fixtures/clean_app/.codelens

# Re-run test — passes
PYTHONPATH=scripts python3 -m pytest tests/test_architecture.py::TestArchitectureBasic::test_auto_scans_on_fresh_workspace -v
# PASSED

Impact

• Intermittent CI failure: test_auto_scans_on_fresh_workspace fails whenever a prior test in the same suite has scanned clean_app and left .codelens behind. In CI, test order is deterministic so this may fail consistently.
• False alarm for contributors: a contributor running the full test suite sees 1 failure that has nothing to do with their changes.
• Not a regression: this is pre-existing. Verified by running the test in isolation (still fails) and cleaning up the fixture (passes).

Fix

Two options:

Option A (recommended): gitignore .codelens in fixture directories

Add to .gitignore:

benchmarks/fixtures/*/.codelens/

This prevents .codelens from being tracked, but doesn't prevent tests from creating it on disk. The architecture test would still fail if .codelens exists on disk.

Option B (better): fix the fresh_clean_app fixture to exclude .codelens when copying

In tests/test_architecture.py, the fixture that creates fresh_clean_app should use shutil.copytree with ignore=shutil.ignore_patterns('.codelens'):

fresh_clean_app = tempfile.mkdtemp()
shutil.copytree(
    clean_app_source,
    fresh_clean_app,
    dirs_exist_ok=True,
    ignore=shutil.ignore_patterns('.codelens', '__pycache__'),
)

This makes the test robust regardless of what other tests leave behind in the fixture directory.

Option C (belt-and-suspenders): both A + B

Gitignore the .codelens dirs (so they don't get committed) AND fix the fixture to exclude them when copying (so test order doesn't matter).

Acceptance criteria

• test_auto_scans_on_fresh_workspace passes even after test_vuln_staleness.py has run in the same suite
• benchmarks/fixtures/*/.codelens/ is gitignored (no fixture-created .codelens dirs tracked)
• No .codelens dirs in any benchmarks/fixtures/ path committed to the repo

Files

• .gitignore (Option A)
• tests/test_architecture.py (Option B — fresh_clean_app fixture)
• Possibly other test files that copy fixture directories

Related

• Discovered while verifying [BUG-02] --deep flag runs HybridEngine twice — LSP findings double-counted #32 and [BUG-P0] check command rejects positional workspace arg - CI quality-gate broken for all PRs #78 fixes (not a regression from either)
• Related pattern: test_compact_format.py and other tests that use clean_app fixture may have the same issue