fix(manifest): fail closed on scan timeout

[mldangelo-oai]

Summary

• mark manifest timeouts as operational errors with incomplete coverage
• return success=False instead of reporting a successful scan
• retain findings emitted before the timeout

Reproduction

ManifestScanner.scan() caught TimeoutError, emitted a failed Manifest Scan Timeout check, then explicitly called finish(success=True). Existing timeout tests asserted the contradictory successful outcome.

Validation

• pytest -q tests/scanners/test_manifest_scanner.py -k timeout (6 passed)
• Ruff format and lint pass on changed Python files
• mypy passes on changed Python files

[github-actions]

Workflow run and artifacts

Performance Benchmarks

Compared 12 shared benchmarks with a regression threshold of 15%.
Status: 0 regressions, 0 improved, 12 stable, 0 new, 0 missing.
Aggregate shared-benchmark median: 1.383s -> 1.391s (+0.6%).

Workload	Benchmark	Target	Size	Files	Baseline	Current	Change	Status
padded-multi-stream-upload	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_padded_multi_stream_upload	multi_stream_padded	4.1 KiB	1	640.2us	597.9us	-6.6%	stable
warm-cache-rescan	tests/benchmarks/test_scan_benchmarks.py::test_scan_warm_cached_repository_rescan	release-candidate	547.3 KiB	32	100.19ms	106.32ms	+6.1%	stable
chunked-upload-stream	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_chunked_upload_stream	chunked_stream	278.2 KiB	1	111.91ms	110.72ms	-1.1%	stable
mixed-model-repository	tests/benchmarks/test_scan_benchmarks.py::test_scan_release_candidate_repository	release-candidate	547.3 KiB	32	471.22ms	475.84ms	+1.0%	stable
nested-payload-review	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_nested_payload_review[nested_raw]	nested_raw	78 B	1	539.2us	544.0us	+0.9%	stable
clean-training-checkpoint	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_clean_training_checkpoint	safe_large	278.2 KiB	1	108.19ms	107.38ms	-0.7%	stable
direct-malicious-upload	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_direct_malicious_upload	malicious_reduce	52 B	1	505.2us	507.9us	+0.5%	stable
nested-payload-review	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_nested_payload_review[nested_hex]	nested_hex	130 B	1	567.6us	564.8us	-0.5%	stable
suspicious-pickle-intake	tests/benchmarks/test_scan_benchmarks.py::test_scan_suspicious_pickle_intake	suspicious-intake	183.8 KiB	4	141.34ms	140.90ms	-0.3%	stable
nested-payload-review	tests/benchmarks/test_picklescan_benchmarks.py::test_picklescan_nested_payload_review[nested_base64]	nested_base64	98 B	1	540.9us	539.8us	-0.2%	stable
single-checkpoint-preflight	tests/benchmarks/test_scan_benchmarks.py::test_scan_single_checkpoint_before_load	single_checkpoint.pkl	183.0 KiB	1	68.59ms	68.67ms	+0.1%	stable
duplicate-heavy-registry	tests/benchmarks/test_scan_benchmarks.py::test_scan_duplicate_registry_snapshot	registry-snapshot	915.2 KiB	13	379.18ms	378.88ms	-0.1%	stable

[mldangelo-oai]

@codex review

Please review exact head SHA 6a23bcf.

[mldangelo-oai]

@codex review

Please review exact head SHA 5a66e63.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Hooray!

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