fix(persistence): refurb cleanups in replay journal + lineage signer + eval (cluster C)

[chernistry]

Summary

Address 7 refurb alerts across 5 files in the replay journal, lineage signer, and eval subsystems.

Alerts cleared

Alert	File:line	Rule	Fix
#2468	src/bernstein/core/persistence/journal.py:209	FURB123	list(self.blob_refs) -> self.blob_refs.copy()
#2469	src/bernstein/core/persistence/journal_export.py:94	FURB123	list(self.blob_digests) -> self.blob_digests.copy()
#2470	src/bernstein/core/persistence/journal_export.py:108	FURB123	list(self.blob_digests) -> self.blob_digests.copy()
#2471	src/bernstein/core/persistence/journal_export.py:485	FURB160	drop redundant JournalError = JournalError self-assignment; add JournalError to __all__ so the re-export stays explicit for callers
#2472	src/bernstein/core/persistence/journal_publish.py:136	FURB123	dict(row) -> row.copy()
#2473	src/bernstein/core/persistence/lineage_signer.py:223	FURB123	list(parents) -> parents.copy()
#2465	src/bernstein/eval/incident_synthesizer.py:756	FURB124	collapse raw[0] == '"' and raw[-1] == '"' into chained raw[0] == '"' == raw[-1]

Behaviour

Unchanged. Each .copy() produces the same shallow-copy semantics as the explicit list(...) / dict(...) constructor. The chained comparison evaluates identically for two-character bounds. The JournalError re-export remains available via the top-of-file import; adding it to __all__ documents the public surface explicitly.

Test plan

• uv run refurb on the 5 touched files is clean.
• uv run pytest tests/unit/ -q --no-cov --timeout=120 -k "journal or lineage_signer or incident_synthesizer" - 104 tests pass.
• uv run ruff check . --fix && uv run ruff format . - all checks passed, no formatting drift.
• uv run pyright on the 5 touched files - error count unchanged versus origin/main baseline (53/53; all pre-existing).

Summary by CodeRabbit

• Bug Fixes

  • Improved handling of quoted strings in YAML parsing.

• Documentation

  • Added schedule command to documented CLI commands list.

• Refactor

  • Updated internal list copying methods across persistence modules.

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[github-actions]

Sonar insights (advisory, no merge-block)

Snapshot of bernstein on the configured Sonar instance:

Metric	Value
Coverage	13.5
Code smells	151
Bugs	11
Vulnerabilities	2
Security hotspots	91

Run bernstein doctor sonar locally for the full surface.

This comment is a soft signal. The Sonar scan runs on push to main; the PR check itself never fails on smells.

[github-actions]

Review-bot acknowledgement summary

• Must-address findings: 0 (0 acknowledged, 0 open)
• Informational findings: 0

All must-address findings are resolved or acknowledged.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro

Run ID: 3c85c97a-34f7-406c-92c9-9998627929c2

📥 Commits

Reviewing files that changed from the base of the PR and between e0b9317 and d8d0799.

📒 Files selected for processing (1)

• tests/unit/test_journal_chain.py

📝 Walkthrough

Walkthrough

PR consolidates shallow copy patterns across persistence and eval modules by replacing type constructors (list(), dict()) with .copy() methods in five locations, adds JournalError to module exports, updates CLI documentation test expectations, and simplifies a quoted-scalar detection condition.

Changes

Code style and API surface updates

Layer / File(s)	Summary
Shallow copy method consolidation across persistence src/bernstein/core/persistence/journal.py, src/bernstein/core/persistence/journal_export.py, src/bernstein/core/persistence/journal_publish.py, src/bernstein/core/persistence/lineage_signer.py	Five functions replace shallow copy constructors with .copy() methods: JournalEntry.to_dict() (line 209), ReceiptManifest.canonical_bytes() (lines 91–96), ReceiptManifest.to_json() (lines 105–110), _redact_row() (line 136), and register_attachment_parents() (line 223).
API export and test expectations src/bernstein/core/persistence/journal_export.py, tests/unit/test_readme_api_coverage.py	journal_export.__all__ (lines 475–482) now explicitly exports JournalError; test_readme_api_coverage.py (lines 242–243) adds "schedule" to DOCUMENTED_COMMANDS allowlist.
YAML quoted-scalar detection simplification src/bernstein/eval/incident_synthesizer.py	_source_incident_from_yaml() (lines 753–758) uses chained equality raw[0] == '"' == raw[-1] instead of separate boolean checks to detect double-quoted scalars.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Suggested labels

tests

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The PR title accurately describes the main change: refurb linter cleanups across five files in persistence and eval subsystems.
Description check	✅ Passed	The PR description comprehensively documents what was changed, why, and how—including a detailed alerts table, behavior notes, and test results—but does not follow the provided template structure.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/code-scanning-cluster-c

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[github-actions]

bernstein doctor observe for PR #1813 (fix/code-scanning-cluster-c): ok=0, warn=2, fail=0, error=0, skipped=2

sonar -- WARN (project bernstein)

metric	value	delta	threshold	status
coverage_pct	13.5%	new	80.0%	fail
code_smells	151	new	50	warn
bugs	11	new	0	fail
vulnerabilities	2	new	0	warn
security_hotspots	91	new	0	fail

code-scanning -- WARN (40 open alert(s))

metric	value	delta	threshold	status
open_alerts	40	new	0	fail
critical_alerts	0	new	0	ok
high_alerts	2	new	0	warn
medium_alerts	0	new	-	ok
low_alerts	0	new	-	ok

Skipped backends (credentials not configured)

• glitchtip: BERNSTEIN_GLITCHTIP_TOKEN not set
• dt: DTRACK_URL/TOKEN/PROJECT not set

See docs/observability/unified-doctor.md for backend setup notes.