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Imbad0202/academic-research-skills

Academic Research Skills for Claude Code: research → write → review → revise → finalize

22.1 Moderate AI signal View on GitHub
22.1
Adjusted Score
22.1
Raw Score
100%
Time Factor
2026-05-30
Last Push
24,509
Stars
Python
Language
140,119
Lines of Code
520
Files
1951
Pattern Hits
2026-05-31
Scan Date

Score History

Severity Breakdown

CRITICAL 0HIGH 37MEDIUM 456LOW 1458

Pattern Findings

1951 matches across 13 categories. Click a row to expand file-level details.

Decorative Section Separators429 hits · 1484 pts
SeverityFileLineSnippet
MEDIUMevals/calibration/commitment_ledger_seed.yaml2# ----------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py134# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py136# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py275# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py277# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py291# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py293# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py311# ---------------------------------------------------------------------------
MEDIUMscripts/policy_anchor_disclosure_referee.py313# ---------------------------------------------------------------------------
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py63# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py65# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py79# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py81# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py106# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py108# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py196# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py198# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py221# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py223# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py247# =========================================================================
MEDIUMscripts/test_check_v3_6_8_cite_provenance_pipeline.py249# =========================================================================
MEDIUMscripts/test_audit_schemas.py37# ---------------------------------------------------------------------------
MEDIUMscripts/test_audit_schemas.py39# ---------------------------------------------------------------------------
MEDIUMscripts/test_audit_schemas.py222# ---------------------------------------------------------------------------
MEDIUMscripts/test_audit_schemas.py224# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py27# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py29# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py49# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py51# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py315# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py317# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py556# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py558# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py582# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py584# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py641# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py643# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py650# ---------------------------------------------------------------------------
MEDIUMscripts/parse_audit_verdict.py652# ---------------------------------------------------------------------------
MEDIUMscripts/test_slr_lineage_emission.py35# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py37# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py98# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py100# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py151# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py153# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py194# ============================================================================
MEDIUMscripts/test_slr_lineage_emission.py196# ============================================================================
MEDIUMscripts/claim_audit_pipeline.py633# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py635# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py51# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py53# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py116# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py121# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py352# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py354# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py673# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py675# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py821# ---------------------------------------------------------------------------
MEDIUMscripts/claim_audit_pipeline.py823# ---------------------------------------------------------------------------
MEDIUMscripts/check_v3_6_8_pattern_protection.py430# =============================================================================
369 more matches not shown…
Hyper-Verbose Identifiers1134 hits · 1045 pts
SeverityFileLineSnippet
LOWtests/test_mark_read_args.py39def test_ars_mark_read_writes_read_log(passport_with_corpus: Path) -> None:
LOWtests/test_mark_read_args.py70def test_ars_mark_read_rejects_zero_keys(passport_with_corpus: Path) -> None:
LOWtests/test_mark_read_args.py85def test_ars_mark_read_rejects_unknown_key(passport_with_corpus: Path) -> None:
LOWtests/test_mark_read_args.py101def test_ars_mark_read_argument_parsing(passport_with_corpus: Path) -> None:
LOW…s/design/2026-05-21-v3.10-183-epistemic-status-spec.md737def classify_claim_audit_result(entry: dict) -> list[dict]:
LOW…design/2026-04-23-ars-v3.6.2-sprint-contract-design.md324def check_structural_invariants(contract: dict) -> list[str]:
LOW…-15-issue-105-contamination-signals-backfill-design.md51def compute_ss_unmatched_signal(entry, ss_client) -> bool | None:
LOWdocs/design/2026-05-05-phase-6.6-scoping-note.md120def test_orchestrator_prompt_contains_audit_artifact_gate():
LOWdocs/design/2026-05-05-phase-6.6-scoping-note.md124def test_orchestrator_prompt_references_all_phase_ids():
LOWdocs/design/2026-05-05-phase-6.6-scoping-note.md140def test_orchestrator_prompt_has_audit_gate_hard_rules():
LOWdocs/design/2026-05-05-phase-6.6-scoping-note.md151def test_orchestrator_prompt_size_within_budget():
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md417def test_integration_passes_against_real_repo():
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md871def test_neg_a_drop_ship_enum(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md919def test_neg_b_disqualifying_rename(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md927def test_neg_c_strip_fallback_case(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md935def test_neg_d_delete_legacy_text(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md946def test_neg_e_remove_policy_fold(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md963def test_neg_f_leak_into_deep_research(tmp_path):
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md990def test_neg_g_carrier_regression(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1024def test_sanitize_strips_non_alnum():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1033def test_sanitize_rejects_empty():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1037def test_make_citation_key_simple():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1044def test_make_citation_key_collision_suffix():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1050def test_make_citation_key_multiple_collisions():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1056def test_parse_csl_name_family_given():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1060def test_parse_csl_name_family_initial():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1064def test_parse_csl_name_institution_with_paren_marker():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1069def test_parse_csl_name_bare_single_token_literal():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1075def test_parse_semicolon_names():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1083def test_parse_semicolon_names_empty_returns_empty_list():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1088def test_dump_yaml_stable_is_sorted():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md149def test_required_set_matches_spec():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md160def test_additional_properties_is_false():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md165def test_valid_personal_author_entry_passes():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md177def test_valid_institution_author_entry_passes():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md189def test_missing_required_field_fails():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md203def test_author_must_be_either_personal_or_literal():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md217def test_year_out_of_range_fails():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md231def test_citation_key_pattern_rejects_leading_digit():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md245def test_additional_property_fails():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md260def test_obtained_via_enum_constrained():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md473def test_schema_self_consistent():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md478def test_empty_rejected_is_valid():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md489def test_missing_required_top_level_fails():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md496def test_rejection_with_object_raw():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md514def test_rejection_with_string_raw():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md531def test_rejection_with_array_raw_rejected():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md550def test_reason_enum_constrained():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md562def test_additional_properties_false_on_rejection():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md738def test_passes_on_valid_passport(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md755def test_fails_on_schema_violation(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md773def test_fails_on_duplicate_citation_key(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md798def test_passes_on_valid_rejection_log(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md810def test_default_mode_scans_repo_examples():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1102def test_adapter_spec_version_is_string():
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1155def _first_title_word_non_stopword(title_hint: str | None) -> str:
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1463def test_empty_folder_emits_empty_passport(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1480def test_missing_input_dir_fails_loud(tmp_path):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1490def test_deterministic_output(tmp_path, load_yaml, clean_timestamps):
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md1501def test_duplicate_collision_handled(tmp_path):
1074 more matches not shown…
Unused Imports155 hits · 140 pts
SeverityFileLineSnippet
LOWconftest.py2
LOWscripts/contamination_signals.py12
LOWscripts/test_text_similarity.py12
LOWscripts/check_v3_8_annotation_literal_sync.py35
LOWscripts/check_policy_anchor_protocol.py40
LOWscripts/policy_anchor_disclosure_referee.py23
LOWscripts/test_check_v3_6_8_cite_provenance_pipeline.py18
LOWscripts/test_check_v3_6_8_cite_provenance_pipeline.py385
LOWscripts/test_audit_schemas.py17
LOWscripts/test_check_v3_7_3_three_layer_citation.py6
LOWscripts/test_check_v3_7_3_three_layer_citation.py10
LOWscripts/sync_adapter_docs.py18
LOWscripts/test_check_ci_pytest_manifest.py18
LOWscripts/test_check_v3_8_annotation_literal_sync.py17
LOWscripts/test_check_version_consistency.py2
LOWscripts/test_check_spec_consistency.py9
LOWscripts/check_pattern_eval_manifest.py23
LOWscripts/parse_audit_verdict.py17
LOWscripts/test_check_v3_9_2_phase_boundary.py5
LOWscripts/check_rq_framing_patterns.py8
LOWscripts/test_run_ci_pytest_manifest.py13
LOWscripts/test_temporal_integrity_audit.py2
LOWscripts/test_temporal_integrity_audit.py4
LOWscripts/test_check_sprint_contract.py2
LOWscripts/check_literature_corpus_schema.py22
LOWscripts/check_literature_corpus_schema.py32
LOWscripts/test_slr_lineage_emission.py21
LOWscripts/claim_audit_pipeline.py17
LOWscripts/_passport_yaml.py27
LOWscripts/check_v3_6_8_pattern_protection.py44
LOWscripts/test_pattern_eval_runtime.py26
LOWscripts/test_pattern_eval_runtime.py31
LOWscripts/check_v3_6_8_mark_read_commands.py12
LOWscripts/test__next_verified_at_ms.py24
LOWscripts/openalex_client.py10
LOWscripts/openalex_client.py26
LOWscripts/openalex_client.py34
LOWscripts/crossref_client.py15
LOWscripts/crossref_client.py28
LOWscripts/crossref_client.py36
LOWscripts/test_audit_snapshot_render_section_0.py14
LOWscripts/test_audit_snapshot_render_section_0.py18
LOWscripts/test_check_policy_anchor_table.py10
LOWscripts/ars_mark_read.py24
LOWscripts/test_check_collaboration_depth_rubric.py2
LOWscripts/test_uncited_assertion.py17
LOWscripts/test_policy_anchor_disclosure.py21
LOWscripts/check_repro_lock.py11
LOWscripts/test_check_v3_6_8_audit_scope_block.py31
LOWscripts/test_ars_mark_read.py13
LOWscripts/_skill_lint.py7
LOWscripts/check_v3_7_3_three_layer_citation.py33
LOWscripts/test_check_pattern_eval_manifest.py15
LOWscripts/check_preprint_venues_consistency.py23
LOWscripts/test_check_v3_9_0_triangulation.py3
LOWscripts/test_check_v3_9_0_triangulation.py9
LOWscripts/test_check_v3_6_8_pattern_protection.py20
LOWscripts/test_check_v3_6_8_pattern_protection.py23
LOWscripts/test_check_v3_6_8_pattern_protection.py24
LOWscripts/test_check_v3_6_8_pattern_protection.py29
95 more matches not shown…
Synthetic Comment Markers16 hits · 88 pts
SeverityFileLineSnippet
HIGHacademic-paper/references/policy_anchor_table.md80- Field #16 mandate produces a paragraph noting (a) appropriate attribution + full citations for AI-quoted material, (b)
HIGHacademic-paper/references/policy_anchor_table.md107| 16 | AI-generated image / figure / content rights | explicit-mandate | "Springer Nature journals are unable to permit
HIGHshared/policy_data/nature_policy.md34> "All exceptions must be labelled clearly as generated by AI within the image field."
HIGH…cs/design/2026-05-13-ai-disclosure-schema-discovery.md199| 16 | AI-generated image / figure / content rights | explicit-mandate | "Springer Nature journals are unable to permit
HIGH…cs/design/2026-05-13-ai-disclosure-schema-discovery.md261- ICMJE #16 = text-attribution clause; Nature #16 = default-prohibit + 3 carve-outs + labelling-required; IEEE #16 = fol
HIGH…cs/design/2026-05-13-ai-disclosure-schema-discovery.md383- Nature #16 image-rights regime requires labelling text "generated by AI" at the location "within the image field" (ver
HIGHdocs/design/2026-05-14-ai-disclosure-impl-spec.md83| 4 | IEEE section locator shape | Free-form list with recommended IMRaD exemplars (parallel to G8 `level_of_involvement
HIGHdocs/design/2026-05-14-ai-disclosure-schema-decision.md213**Companion mandate — IEEE #6 affected sections locator.** IEEE #5 ("level") is paired with IEEE #6 ("specific sections
HIGHdocs/design/2026-05-14-ai-disclosure-schema-decision.md219**Rationale.** §4.4 ICMJE #16 (text-attribution rule, no-AI-as-primary-source — mandate), §4.5 Nature #16 (default-prohi
HIGHdocs/design/2026-05-14-ai-disclosure-schema-decision.md2934. **Renderer input contract — IEEE section locator.** IEEE #6 is explicit-mandate on "specific sections of the article
HIGHdocs/design/2026-05-14-ai-disclosure-schema-decision.md2945. **Renderer input contract — Nature image metadata.** Nature #16 default-deny + 3 carve-outs + labelling requires per-
HIGH…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html219 </a></div> <div class="container"><div class="row"><div class="col-lg-3 mb-5 sidebar-sections"><div
HIGH…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html219 </a></div> <div class="container"><div class="row"><div class="col-lg-3 mb-5 sidebar-sections"><div
HIGH…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html321 </p></div></div></div></footer></section></div></div> <div><a tabindex="0" href="javascript:;" t
HIGH…apshots/2026-05-13-ai-disclosure-discovery/nature.html713<p>*All exceptions must be labelled clearly as generated by AI within the image field.</p>
HIGH…ademic-pipeline/agents/integrity_verification_agent.md64- Walters, W. H., & Wilder, E. I. (2023). Fabrication and errors in the bibliographic citations generated by ChatGPT. *S
Cross-Language Confusion12 hits · 76 pts
SeverityFileLineSnippet
HIGHscripts/claim_audit_pipeline.py593 # U-INV-4 (manifest_claim_id null ↔ scoped_manifest_id null).
HIGHscripts/claim_audit_finalizer.py175 # synthesis_overclaim, null} on AMBIGUOUS — the §6 consistency lint is
HIGHscripts/check_repro_lock.py6- Missing `repro_lock` key (not even null): ERROR, exit 1.
HIGHscripts/check_v3_6_8_frontmatter_trust_schema.py154 # null). Round-6 codex P2 closure tightened the value to the literal
HIGHscripts/test_check_passport_reset_contract.py145 # Binary bytes (0xff, 0xfe, null) fail UTF-8 decode; the lint must
HIGHscripts/test_claim_audit_finalizer.py167# T-F1b — AMBIGUOUS + {source_description, citation_anchor, synthesis_overclaim, null}
HIGHscripts/test_check_v3_6_8_frontmatter_trust_schema.py157# ---------- Rule #2 — source_acquired=false → description_last_audit ∈ {null, 'none'} ----------
HIGHscripts/test_claim_audit_schema.py412 # INV-9: upstream_dispute != null -> defect_stage NOT in {null, not_applicable}
HIGHscripts/check_evals_gold_set.py171 errors.append(f"I6: {stem}.json kind={kind!r} but arxiv_id={arxiv_id!r} present (must be null)")
HIGHscripts/check_claim_audit_consistency.py930 # CV-INV-3: MNC -> manifest_claim_id null; NC -> manifest_claim_id non-null and matches.
HIGHscripts/migrate_literature_corpus_to_v3_7_3.py75 the spec rule are undefined). Schema marks `year` as required so this
HIGHscripts/check_audit_artifact_consistency.py2069 # passed `[]` / a scalar / null) would crash check_e3_e4 with
Over-Commented Block87 hits · 75 pts
SeverityFileLineSnippet
LOWevals/calibration/commitment_ledger_seed.yaml1# Kong A1 / v3.11 — Commitment Ledger Calibration Seed
LOWevals/calibration/commitment_ledger_seed.yaml21# P1 (1 case): single-commitment, partial (evidence-exists-but-incomplete, with rationale)
LOW…026-04-30-ars-v3.6.7-step-6-orchestrator-hooks-spec.md661}
LOW…026-04-30-ars-v3.6.7-step-6-orchestrator-hooks-spec.md701# fsyncs the tmp file, then renames it over <path>. Used for sidecar, verdict,
LOW…026-04-30-ars-v3.6.7-step-6-orchestrator-hooks-spec.md721 fi
LOW…026-04-30-ars-v3.6.7-step-6-orchestrator-hooks-spec.md801 "${supporting_args[@]}" \
LOW…026-04-30-ars-v3.6.7-step-6-orchestrator-hooks-spec.md821#
LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md761 f: list[str] = []
LOW…shots/2026-05-13-ai-disclosure-discovery/manifest.yaml101# anchor below, re-compute the SHA-256 of the local HTML and confirm it matches the value here.
LOWscripts/check_v3_8_annotation_literal_sync.py181 # Closed literals end in `]` and require exact byte-equivalent
LOWscripts/test_check_spec_consistency.py41
LOWscripts/test_check_spec_consistency.py61### v3.6.7 (2026-04-30) — pattern protection
LOWscripts/test_check_spec_consistency.py121### v3.9.4（2026-05-18）— temporal verification
LOWscripts/test_check_spec_consistency.py181
LOWscripts/parse_audit_verdict.py321# Form A (findings present):
LOWscripts/claim_audit_pipeline.py1141 # so a drifted-yet-violated citation does not produce a
LOWscripts/claim_audit_pipeline.py1161 # a sentence-level `scoped_manifest_id`. Pre-fix this loop required the
LOWscripts/claim_audit_pipeline.py1221 continue
LOWscripts/_ci_pytest_manifest.toml1# CI pytest invocation manifest (issue #156)
LOWscripts/check_v3_6_8_pattern_protection.py321 # the hashed range (round-8 closure: BOM-before-heading mutation
LOWscripts/check_v3_6_8_pattern_protection.py421 files = data.get("files")
LOWscripts/check_v3_6_8_pattern_protection.py441# Block scope: starts at the H2 line `## Two-Layer Citation Emission (v3.7.1)`
LOWscripts/check_v3_6_8_pattern_protection.py461 re.compile(_NON_IDENT_BEFORE + r"finalizers?" + _NON_IDENT_AFTER, re.IGNORECASE),
LOWscripts/check_v3_6_8_pattern_protection.py481# Whitespace between verb and target spans `\s` (newline + indent) not just
LOWscripts/check_v3_6_8_pattern_protection.py521 r"cannot|can'?t|may\s+not|shall\s+not|forbidden|"
LOWscripts/test_pattern_eval_runtime.py101 # a subsequent candidate succeeds; the rule is the orchestrator commits at most
LOWscripts/check_v3_7_3_three_layer_citation.py141 """Return a list of violation strings; empty list = PASS."""
LOWscripts/check_v3_7_3_three_layer_citation.py221 f"percent-encoded as `%2D` to prevent premature HTML "
LOWscripts/test_check_v3_6_8_pattern_protection.py581 assert _strip_file_bom(b"hi\xef\xbb\xbfworld") == b"hi\xef\xbb\xbfworld"
LOWscripts/claim_audit_calibration.py21from typing import Any, Callable
LOWscripts/check_v3_6_8_audit_scope_block.py101# Forbidden combined-aggregate "PASSED" verb in audit summary contexts.
LOWscripts/check_v3_6_8_audit_scope_block.py301 # N — Scope Report"`) inside Section 0 must NOT satisfy the contract.
LOWscripts/check_v3_6_8_audit_scope_block.py361
LOWscripts/check_v3_6_8_audit_scope_block.py381 # post-Section-0 surface violates the spec line 152 contract. Quoted
LOWscripts/_claim_audit_constants.py41DRIFT_RULE_VERSION = "D4-a-v1"
LOWscripts/_claim_audit_constants.py61# of truth — a spec bump touches one literal, not three.
LOWscripts/_claim_audit_constants.py81# context proves them to be years, version triples, or section numbers
LOWscripts/_claim_audit_constants.py101# R1 P1-3). Applied AFTER RE_NUMERIC_QUANTIFIER to the matched substring +
LOWscripts/_claim_audit_constants.py121RE_VERSION_PREFIX = re.compile(r"v\s*$", re.IGNORECASE)
LOWscripts/_claim_audit_constants.py141# R0 `[^-]+` — rejected hyphenated slugs.
LOWscripts/semantic_scholar_client.py201 f"S2 API HTTP {e.code} after {_MAX_RETRIES} retries"
LOWscripts/check_v3_6_7_pattern_protection.py41# Markdown heading pattern that closes a `block_marker` scope. A check's scope
LOWscripts/check_v3_6_7_pattern_protection.py101 # `optional` only counts as a weakener when it directly modifies an
LOWscripts/check_v3_6_7_pattern_protection.py121 # (`will`, `would`, `ought to`) and the advisory adverb framings
LOWscripts/check_v3_6_7_pattern_protection.py301 # Reject if the bullet/paragraph containing the match carries
LOWscripts/check_v3_6_7_pattern_protection.py401 # "ask upstream for advice" was previously accepted).
LOWscripts/check_v3_6_7_pattern_protection.py541 target=SYNTHESIS_AGENT,
LOWscripts/check_v3_6_7_pattern_protection.py741 (
LOWscripts/check_v3_6_7_pattern_protection.py781# ---------------------------------------------------------------------------
LOWscripts/check_v3_6_7_pattern_protection.py801# inside is tolerant (collapse whitespace runs to a single space) so a future
LOWscripts/uncited_assertion_detector.py101 # Three-or-more-segment dotted forms are unambiguously version
LOWscripts/uncited_assertion_detector.py121 # Two reattachment shapes:
LOWscripts/announce-ars-loaded.sh1#!/usr/bin/env bash
LOWscripts/announce-ars-loaded.sh21set -euo pipefail
LOWscripts/check_claim_audit_consistency.py1061 # UAF-INV-5: rationale MUST begin with this row's own fault_class
LOWscripts/test_v3_6_7_phase_6_6.py41# from main commit 02b87ae (the last main commit before any Phase 6.6 prompt
LOWscripts/test_v3_6_7_phase_6_6.py61# + L3-2 contamination annotation matrix + updated resolution order +
LOWscripts/test_v3_6_7_phase_6_6.py81LINE_BUDGET_V3_8_AUDIT_GATE = 60
LOWscripts/run_codex_audit.sh1#!/usr/bin/env bash
LOWscripts/run_codex_audit.sh21# [--dry-run] # validate inputs only; write nothing
27 more matches not shown…
AI Slop Vocabulary25 hits · 70 pts
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MEDIUMevals/calibration/commitment_ledger_seed.yaml4# trigger (re_review_mode_protocol step 5) once #263 Phase 1b harness
MEDIUMevals/calibration/commitment_ledger_seed.yaml34# Pass criterion (when harness arrives via #263):
MEDIUMevals/calibration/commitment_ledger_seed.yaml35# For each case, harness output must match expected_commitment_gap (boolean),
MEDIUM…contracts/passport/literature_corpus_entry.schema.json127 "description": "v3.7.1 trust-chain field. Method used to verify the entry against the original source. 'none' mean
MEDIUM…contracts/passport/literature_corpus_entry.schema.json190 "description": "v3.7.1 spec §3.1 firm rule #1 (round-2 R2-007 amend): source_verified_against_original=true REQUIR
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html1<!doctype html><html data-n-head-ssr lang="en" data-n-head="%7B%22lang%22:%7B%22ssr%22:%22en%22%7D%7D"><head ><meta data
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html219 </a></div> <div class="container"><div class="row"><div class="col-lg-3 mb-5 sidebar-sections"><div
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html219 </a></div> <div class="container"><div class="row"><div class="col-lg-3 mb-5 sidebar-sections"><div
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html219 </a></div> <div class="container"><div class="row"><div class="col-lg-3 mb-5 sidebar-sections"><div
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html321 </p></div></div></div></footer></section></div></div> <div><a tabindex="0" href="javascript:;" t
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html321 </p></div></div></div></footer></section></div></div> <div><a tabindex="0" href="javascript:;" t
MEDIUM…/2026-05-13-ai-disclosure-discovery/prisma-trAIce.html321 </p></div></div></div></footer></section></div></div> <div><a tabindex="0" href="javascript:;" t
MEDIUMscripts/test_pattern_eval_runtime.py626 # B10/B11 always appends to passport per §5.6 — the harness emulates this.
MEDIUMscripts/test_pattern_eval_runtime.py763 # NO new passport append per §5.6 A7 invariant). The harness models this
MEDIUMscripts/test_pattern_eval_runtime.py838 # MINOR not exercised by this curated subset; harness simplifies to MATERIAL/PASS.
MEDIUMscripts/test_check_audit_artifact_consistency.py2043# Example validation harness (F4) — smoke test it runs without crash
MEDIUMscripts/test_check_audit_artifact_consistency.py2054 # harness should surface. We only assert the harness ran and any
MEDIUMscripts/test_check_audit_artifact_consistency.py1941 # and confirm it produces the documented harness exit code. Belt
MEDIUMscripts/check_audit_artifact_consistency.py1737# §3.7 F4 example-validation harness
MEDIUMscripts/check_audit_artifact_consistency.py1845 # The harness's job is to surface drift in §3.1/§3.3/§3.4/§3.5
MEDIUMscripts/check_audit_artifact_consistency.py2012 # (e.g., schematic '...' placeholders the harness intentionally skips)
MEDIUMscripts/check_audit_artifact_consistency.py163 mode: str # "proposal" | "persisted" | "jsonl-stream" | "harness"
MEDIUM.github/workflows/harness-retirement-monthly.yml8# harness-retirement skill exists but hasn't been run against ARS
MEDIUM.github/workflows/harness-retirement-monthly.yml15# `/harness-retirement` and paste results into.
MEDIUM.github/workflows/spec-consistency.yml346 # docs/design/2026-05-21-v3.10-184-extend-eval-harness-spec.md.
Cross-File Repetition9 hits · 45 pts
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HIGHscripts/test_check_ci_pytest_manifest.py0jobs: spec: runs-on: ubuntu-latest steps: - run: python scripts/run_ci_pytest_manifest.py
HIGHscripts/test_check_ci_pytest_manifest.py0jobs: spec: runs-on: ubuntu-latest steps: - run: python scripts/run_ci_pytest_manifest.py
HIGHscripts/test_check_ci_pytest_manifest.py0jobs: spec: runs-on: ubuntu-latest steps: - run: python scripts/run_ci_pytest_manifest.py
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
HIGHscripts/test_check_ci_pytest_manifest.py0[[pytest]] id = "real-a" path = "scripts/test_real_a.py"
Deep Nesting46 hits · 36 pts
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LOWscripts/parse_audit_verdict.py443
LOWscripts/check_rq_framing_patterns.py85
LOWscripts/claim_audit_pipeline.py444
LOWscripts/claim_audit_pipeline.py638
LOWscripts/claim_audit_pipeline.py826
LOWscripts/test_pattern_eval_runtime.py191
LOWscripts/test_pattern_eval_runtime.py606
LOWscripts/openalex_client.py80
LOWscripts/crossref_client.py106
LOWscripts/check_v3_6_8_frontmatter_trust_schema.py81
LOWscripts/check_domain_evidence_profile.py311
LOWscripts/check_pipeline_integrity.py133
LOWscripts/check_pipeline_integrity.py205
LOWscripts/claim_audit_calibration.py75
LOWscripts/claim_audit_calibration.py213
LOWscripts/check_version_consistency.py104
LOWscripts/check_v3_6_6_ab_manifest.py74
LOWscripts/check_v3_6_6_ab_manifest.py262
LOWscripts/check_v3_6_7_pattern_protection.py1147
LOWscripts/uncited_assertion_detector.py68
LOWscripts/check_corpus_consumer_protocol.py252
LOWscripts/temporal_integrity_audit.py188
LOWscripts/temporal_integrity_audit.py275
LOWscripts/temporal_integrity_audit.py468
LOWscripts/temporal_integrity_audit.py559
LOWscripts/test_claim_audit_schema.py837
LOWscripts/check_evals_gold_set.py51
LOWscripts/check_claim_audit_consistency.py551
LOWscripts/check_claim_audit_consistency.py656
LOWscripts/check_claim_audit_consistency.py761
LOWscripts/check_claim_audit_consistency.py850
LOWscripts/check_claim_audit_consistency.py1124
LOWscripts/migrate_literature_corpus_to_v3_7_3.py88
LOWscripts/migrate_literature_corpus_to_v3_9_0.py72
LOWscripts/test_claim_audit_pipeline.py392
LOWscripts/check_passport_reset_contract.py113
LOWscripts/check_audit_artifact_consistency.py274
LOWscripts/check_audit_artifact_consistency.py453
LOWscripts/check_audit_artifact_consistency.py807
LOWscripts/check_audit_artifact_consistency.py1011
LOWscripts/check_audit_artifact_consistency.py1412
LOWscripts/check_audit_artifact_consistency.py1645
LOWscripts/check_audit_artifact_consistency.py1741
LOWscripts/check_audit_artifact_consistency.py1787
LOWscripts/check_audit_artifact_consistency.py2001
LOWscripts/adapters/zotero.py143
Excessive Try-Catch Wrapping24 hits · 22 pts
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LOW…n/2026-05-30-kong-259-domain-evidence-profiles-plan.md808 except Exception as exc:
LOW…26-04-23-ars-v3.6.4-literature-corpus-adapters-plan.md884 except Exception as e:
LOWscripts/check_literature_corpus_schema.py54 except Exception as e:
LOWscripts/claim_audit_pipeline.py263 except Exception as exc: # noqa: BLE001 — translation boundary; the source class is captured
LOWscripts/claim_audit_pipeline.py308 except Exception as exc: # noqa: BLE001 — translation boundary
LOWscripts/check_repro_lock.py87 except Exception as exc:
LOWscripts/test_run_codex_audit_e2e.py60 except Exception: # pragma: no cover - defensive
MEDIUMscripts/test_run_codex_audit_e2e.py51def _bash_major_version() -> int:
LOWscripts/check_domain_evidence_profile.py378 except Exception as exc:
LOWscripts/test_claim_intent_manifest.py47except Exception as exc: # pragma: no cover — RED-phase import pathway
LOWscripts/test_claim_audit_finalizer.py92except Exception as exc: # pragma: no cover
LOWscripts/check_v3_9_4_temporal_verification.py57 except Exception as exc:
LOWscripts/check_v3_9_4_temporal_verification.py71 except Exception:
LOWscripts/check_corpus_consumer_protocol.py388 except Exception as exc:
LOWscripts/bootstrap_timeline_yaml.py42 except Exception:
LOWscripts/bootstrap_timeline_yaml.py61 except Exception:
LOWscripts/test_claim_audit_pipeline.py28except Exception as exc: # pragma: no cover — import-time error pathway is exercised in RED state
LOWscripts/check_audit_artifact_consistency.py1702 except Exception:
LOWscripts/check_audit_artifact_consistency.py1732 except Exception as e: # pragma: no cover
LOWscripts/check_audit_artifact_consistency.py1839 except Exception as e: # pragma: no cover
LOWscripts/check_audit_artifact_consistency.py1975 except Exception:
LOWscripts/check_audit_artifact_consistency.py2193 except Exception as e:
LOWscripts/check_audit_artifact_consistency.py2213 except Exception as e:
LOWscripts/check_audit_artifact_consistency.py2270 except Exception as e:
Verbosity Indicators12 hits · 15 pts
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LOWscripts/test_pattern_eval_runtime.py890 # Step 4: at round-3 escalation, feed user_response.yaml.
LOWscripts/test_pattern_eval_runtime.py919 # Step 5: assert expected_passport_state.yaml matches actual.
LOWscripts/check_domain_evidence_profile.py25INTAKE_STEP12_HEADING = "### Step 12: Domain Evidence Profile"
LOWscripts/test_claim_audit_calibration.py410 # Step 1: validate_gold_set MUST accept the manifest-only tuple
LOWscripts/test_claim_audit_calibration.py413 # Step 2: run_calibration MUST refuse it at run time.
LOWscripts/test_check_domain_evidence_profile.py202 "### Step 12: Domain Evidence Profile",
LOWscripts/test_check_domain_evidence_profile.py203 "### Step 12: Domain Evidence Profile\n\nStore the profile on the Material Passport.",
LOW…/adapters/tests/test_check_corpus_consumer_protocol.py103 ### Step 0: presence detection
LOW…/adapters/tests/test_check_corpus_consumer_protocol.py104 ### Step 1: pre-screen
LOW…/adapters/tests/test_check_corpus_consumer_protocol.py105 ### Step 2: search-fills-gap
LOW…/adapters/tests/test_check_corpus_consumer_protocol.py106 ### Step 3: merge
LOW…/adapters/tests/test_check_corpus_consumer_protocol.py107 ### Step 4: emit report
Self-Referential Comments1 hit · 3 pts
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MEDIUM…/adapters/tests/test_check_corpus_consumer_protocol.py471 # Create the second consumer agent file by cloning bibliography_agent.md content
Example Usage Blocks1 hit · 1 pts
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LOWscripts/run_codex_audit.sh10# Usage: