brycewang-stanford/Auto-Empirical-Research-Skills

Pattern Findings

The scanner identified 5180 distinct pattern matches across 25 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a detector match to inspect in context. Expand any category row to inspect the individual file paths, line numbers, code snippets, and the lexical context (CODE, COMMENT, or STRING) in which each match was detected.

Reading the findings table: The Severity column indicates the configured finding weight (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — legacy comment-context matches receive a ×1.5 score weight. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier under the legacy scoring model.

Decorative Section Separators973 hits · 3120 pts

Severity	File	Line	Snippet	Context
MEDIUM	benchmark/lib/structural.py	82	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/structural.py	84	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/structural.py	137	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/structural.py	139	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/structural.py	197	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/structural.py	199	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/spillover.py	133	# --------------------------------------------------------------------------	COMMENT
MEDIUM	benchmark/lib/spillover.py	135	# --------------------------------------------------------------------------	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	24	# ── SSL safety net — use certifi CA bundle ─────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	31	# ── Paths ────────────────────────────────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	41	# ── Helper helpers ──────────────────────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	105	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	107	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	324	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	326	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	331	# ── 4a. IV analysis ──────────────────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	386	# ── 4b. Progressive controls (OLS) ───────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	433	# ── 4c. Design horse race ──────────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	587	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	589	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	597	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	599	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	604	# ── 7.1 Placebo — re75 as outcome ───────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	612	# ── 7.2 Oster (2019) δ bounds ─────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	633	# ── 7.3 Sensitivity dashboard ──────────────────────────────	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	770	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/statsPAI_pipeline_5.2.py	772	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	130	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	132	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	160	# ── Data contract ────────────────────────────────────────────────	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	179	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	181	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	232	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	234	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	281	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	283	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	523	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	525	# ════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	657	# ── 7.4 Robustness master (Table A1) ───────────────────────	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	740	# ── 7.5 Specification curve ────────────────────────────────	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	831	# ── Directory listing ──────────────────────────────────────────	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	32	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	34	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	71	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	73	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	97	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	99	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	122	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	124	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	172	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	174	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	207	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	209	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	219	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM⚡	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	221	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	291	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/_r_pipeline_outputs/_runner_v2.R	293	# ════════════════════════════════════════════════════════════════════════════════	COMMENT
MEDIUM	demo-notebooks/nsw-lalonde-1986/replicate_nsw.py	70	# --------------------------------------------------------------------------	COMMENT
MEDIUM	demo-notebooks/nsw-lalonde-1986/replicate_nsw.py	72	# --------------------------------------------------------------------------	COMMENT
MEDIUM	demo-notebooks/nsw-lalonde-1986/replicate_nsw.py	101	# --------------------------------------------------------------------------	COMMENT
913 more matches not shown…

Structural Annotation Overuse1753 hits · 3082 pts

Severity	File	Line	Snippet	Context
LOW	…ins/empirical-analysis-python/skills/pipeline/SKILL.md	1236	# Step 1: M = a1 + b·T + ε (does T affect M?)	COMMENT
LOW	…ins/empirical-analysis-python/skills/pipeline/SKILL.md	1237	# Step 2: Y = a2 + c'·T + d·M + ε (direct effect of T holding M fixed)	COMMENT
LOW⚡	…is-r/skills/pipeline/references/07-further-analysis.md	202	# Step 1: fit M ~ T + X	COMMENT
LOW⚡	…is-r/skills/pipeline/references/07-further-analysis.md	205	# Step 2: fit Y ~ T + M + X	COMMENT
LOW⚡	…is-r/skills/pipeline/references/07-further-analysis.md	208	# Step 3: mediate	COMMENT
LOW⚡	docs/05-统计分析与因果推断.md	98	## Step 1: 平行趋势检验	COMMENT
LOW⚡	docs/05-统计分析与因果推断.md	102	## Step 2: 基准回归	COMMENT
LOW⚡	docs/05-统计分析与因果推断.md	106	## Step 3: 稳健性检验（至少4项）	COMMENT
LOW⚡	docs/05-统计分析与因果推断.md	112	## Step 4: 异质性分析	COMMENT
LOW⚡	docs/05-统计分析与因果推断.md	115	## Step 5: 机制分析	COMMENT
LOW⚡	docs/en/05-statistical-analysis-and-causal-inference.md	98	## Step 1: Parallel-Trends Test	COMMENT
LOW⚡	docs/en/05-statistical-analysis-and-causal-inference.md	102	## Step 2: Baseline Regression	COMMENT
LOW⚡	docs/en/05-statistical-analysis-and-causal-inference.md	106	## Step 3: Robustness Checks (at least 4)	COMMENT
LOW⚡	docs/en/05-statistical-analysis-and-causal-inference.md	112	## Step 4: Heterogeneity Analysis	COMMENT
LOW⚡	docs/en/05-statistical-analysis-and-causal-inference.md	115	## Step 5: Mechanism Analysis	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	105	### Step 0: Backup and Clean	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	111	### Step 1: Initialize Project	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	126	### Step 2: Generate math_commands.tex	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	139	### Step 3: Write Each Section	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	210	### Step 4: Build Bibliography	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	268	### Step 5: De-AI Polish and Clarity Pass	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	293	### Step 6: Cross-Review with REVIEWER_MODEL	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	321	### Step 7: Reverse Outline Test (from Research-Paper-Writing-Skills)	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/paper-write/SKILL.md	331	### Step 8: Final Checks	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	40	### Step 1: Gather Proof Context	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	57	### Step 2: Normalize the Claim	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	72	### Step 3: Feasibility Triage	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	87	### Step 4: Build a Dependency Map	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	106	### Step 5: Write the Proof Document	COMMENT
LOW	skills/42-wanshuiyin-ARIS/skills/proof-writer/SKILL.md	137	### Step 6: Final Verification	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	48	### Step 1: Gather Derivation Context	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	66	### Step 2: Freeze the Target	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	78	### Step 3: Choose the Invariant Object	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	95	### Step 4: Normalize Assumptions and Notation	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	111	### Step 5: Classify the Derivation Steps	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	121	### Step 6: Build a Derivation Map	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	139	### Step 7: Write the Derivation Document	COMMENT
LOW	…/42-wanshuiyin-ARIS/skills/formula-derivation/SKILL.md	171	### Step 8: Final Verification	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	81	### Step 0: Backup and Clean	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	87	### Step 1: Initialize Project	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	102	### Step 2: Generate math_commands.tex	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	115	### Step 3: Write Each Section	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	178	### Step 4: Build Bibliography	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	234	### Step 5: De-AI Polish (from kgraph57/paper-writer-skill)	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	249	### Step 6: Cross-Review with REVIEWER_MODEL	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	276	### Step 7: Reverse Outline Test (from Research-Paper-Writing-Skills)	COMMENT
LOW	…skills/skills-codex-claude-review/paper-write/SKILL.md	286	### Step 8: Final Checks	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	45	### Step 1: Read Figure Plan	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	61	### Step 2: Set Up Plotting Environment	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	98	### Step 3: Auto-Select Figure Type	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	113	### Step 4: Generate Each Figure	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	173	### Step 5: Run All Scripts	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	184	### Step 6: Generate LaTeX Include Snippets	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	200	### Step 7: Figure Quality Review with REVIEWER_MODEL	COMMENT
LOW	…kills/skills-codex-claude-review/paper-figure/SKILL.md	221	### Step 8: Quality Checklist	COMMENT
LOW	…/skills/skills-codex-claude-review/paper-plan/SKILL.md	31	### Step 1: Extract Claims and Evidence	COMMENT
LOW	…/skills/skills-codex-claude-review/paper-plan/SKILL.md	49	### Step 2: Determine Paper Type and Structure	COMMENT
LOW	…/skills/skills-codex-claude-review/paper-plan/SKILL.md	93	### Step 3: Section-by-Section Planning	COMMENT
LOW	…/skills/skills-codex-claude-review/paper-plan/SKILL.md	143	### Step 4: Figure Plan	COMMENT
LOW	…/skills/skills-codex-claude-review/paper-plan/SKILL.md	164	### Step 5: Citation Scaffolding	COMMENT
1693 more matches not shown…

Hyper-Verbose Identifiers1099 hits · 1210 pts

Severity	File	Line	Snippet	Context
LOW	benchmark/check_benchmark.py	183	def validate_candidate_dir_name(value: object, label: str = "candidate") -> list[str]:	CODE
LOW	benchmark/check_benchmark.py	193	def validate_repo_relative_file(value: object, label: str) -> list[str]:	CODE
LOW	benchmark/lib/oaxaca.py	132	def explained_reference_swing(rows: list[dict]) -> float:	CODE
LOW	benchmark/lib/spillover.py	209	def true_total_effect_on_treated(rows: list[dict]) -> float:	CODE
LOW	benchmark/lib/bunching.py	52	def _renormalized_counterfactual(bunch_at_K: float, support: list[int]) -> list[float]:	CODE
LOW	benchmark/lib/bunching.py	108	def counterfactual_density_at(rows: list[dict], x: int) -> float:	CODE
LOW	eval-harness/run_evals.py	95	def validate_repo_relative_path(	CODE
LOW	eval-harness/run_evals.py	599	def parse_expected_categories(raw: str \| None) -> set[str]:	CODE
LOW⚡	tests/test_scan_collections.py	64	def test_rm_without_both_flags_is_not_flagged(self):	CODE
LOW⚡	tests/test_scan_collections.py	73	def test_cryptominer_and_input_capture(self):	CODE
LOW⚡	tests/test_scan_collections.py	77	def test_prompt_injection_marker(self):	CODE
LOW⚡	tests/test_scan_collections.py	96	def test_rm_of_a_specific_path_under_home_or_root(self):	CODE
LOW⚡	tests/test_scan_collections.py	106	def test_decoding_without_executing(self):	CODE
LOW⚡	tests/test_scan_collections.py	116	def test_compile_used_for_syntax_checking(self):	CODE
LOW⚡	tests/test_scan_collections.py	130	def test_a_real_embedded_image_still_matches(self):	CODE
LOW⚡	tests/test_scan_collections.py	139	def test_every_collection_on_disk_has_a_record(self):	CODE
LOW⚡	tests/test_scan_collections.py	149	def test_the_gap_that_motivated_this_is_closed(self):	CODE
LOW⚡	tests/test_scan_collections.py	157	def test_no_untriaged_findings_remain(self):	CODE
LOW⚡	tests/test_scan_collections.py	166	def test_every_triage_entry_carries_a_substantive_reason(self):	CODE
LOW⚡	tests/test_scan_collections.py	174	def test_no_triage_entry_is_stale(self):	CODE
LOW	tests/test_scan_collections.py	189	def test_the_record_states_what_the_scan_is_not(self):	CODE
LOW	tests/test_scan_collections.py	197	def test_validate_asserts_the_record_is_current(self):	CODE
LOW	tests/test_scan_collections.py	218	def test_the_scan_reads_git_tracked_files(self):	CODE
LOW⚡	tests/test_scan_collections.py	229	def test_tracked_listing_excludes_untracked_and_ignored_paths(self):	CODE
LOW⚡	tests/test_scan_collections.py	237	def test_the_submodule_contributes_files(self):	CODE
LOW⚡	tests/test_scan_collections.py	247	def test_two_consecutive_scans_agree(self):	CODE
LOW⚡	tests/test_scan_collections.py	252	def test_no_collection_is_silently_empty(self):	CODE
LOW	tests/test_skillopt_gates.py	19	def test_core_empirical_skills_keep_validation_gate(self):	CODE
LOW	tests/test_validate_workflows.py	35	def test_current_repo_workflows_pass_policy(self):	CODE
LOW	tests/test_validate_workflows.py	39	def test_pull_request_write_permissions_fail(self):	CODE
LOW	tests/test_validate_workflows.py	59	def test_scheduled_write_permissions_are_allowed_for_sync_workflows(self):	CODE
LOW	tests/test_validate_workflows.py	81	def test_pull_request_write_all_fails(self):	CODE
LOW	tests/test_validate_workflows.py	99	def test_floating_or_missing_action_refs_fail(self):	CODE
LOW	tests/test_validate_workflows.py	121	def test_local_actions_and_docker_images_are_not_ref_pinned(self):	CODE
LOW	tests/test_split.py	36	def test_frontmatter_preserved(self):	STRING
LOW	tests/test_split.py	54	def test_big_section_is_moved(self):	STRING
LOW	tests/test_split.py	63	def test_apply_preserves_content_and_source(self):	STRING
LOW	tests/test_check_links.py	17	def test_markdown_code_fences_are_skipped_by_default(self):	CODE
LOW	tests/test_check_links.py	39	def test_html_links_and_repeated_files_are_normalized(self):	CODE
LOW	tests/test_check_links.py	61	def test_main_can_write_or_skip_report(self):	CODE
LOW	tests/test_check_links.py	97	def test_main_returns_failure_for_broken_links(self):	CODE
LOW	tests/test_check_links.py	132	def test_the_two_gated_paths_are_recognized(self):	CODE
LOW	tests/test_check_links.py	141	def test_public_github_paths_are_not_exempt(self):	CODE
LOW	tests/test_check_links.py	153	def test_the_pattern_is_anchored_to_github_com(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	57	def test_shares_leave_room_for_an_outside_good(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	67	def test_the_hidden_shock_is_orthogonal_to_the_instruments(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	76	def test_price_is_correlated_with_the_hidden_shock(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	91	def test_iv_recovers_the_design_parameter_exactly(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	94	def test_oracle_regression_recovers_the_same_truth(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	99	def test_ols_is_biased_toward_zero(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	106	def test_the_instrument_is_strong(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	109	def test_elasticity_is_not_the_coefficient(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	117	def test_elasticity_formula_uses_one_minus_share(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	125	def test_marginal_cost_is_below_price(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	132	def test_biased_demand_propagates_into_the_cost_estimate(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	171	def test_quoting_the_coefficient_as_an_elasticity_fails(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	178	def test_skipping_the_instrument_fails(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	187	def test_reading_price_as_marginal_cost_fails(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	197	def test_fabricated_numbers_fail_the_honest_golds(self):	CODE
LOW⚡	tests/test_structural_benchmark.py	209	def test_taxonomy_has_structural_keywords(self):	CODE
1039 more matches not shown…

Cross-File Repetition85 hits · 425 pts

Severity	File	Line	Snippet	Context
HIGH	…ins/empirical-analysis-python/skills/pipeline/SKILL.md	0	return a go/no-go dict. stop the pipeline if any required check fails.	STRING
HIGH	…lls/00.1-Full-empirical-analysis-skill_Python/SKILL.md	0	return a go/no-go dict. stop the pipeline if any required check fails.	STRING
HIGH	…lls/00-Full-empirical-analysis-skill_StatsPAI/SKILL.md	0	return a go/no-go dict. stop the pipeline if any required check fails.	STRING
HIGH	skills/42-wanshuiyin-ARIS/skills/paper-poster/SKILL.md	0	add png image, auto-calculate height from aspect ratio.	STRING
HIGH	…shuiyin-ARIS/skills/skills-codex/paper-poster/SKILL.md	0	add png image, auto-calculate height from aspect ratio.	STRING
HIGH	…kills/skills-codex-gemini-review/paper-poster/SKILL.md	0	add png image, auto-calculate height from aspect ratio.	STRING
HIGH	…ills/67-econfin-workflow-toolkit/data-fetcher/SKILL.md	0	economic data fetcher ===================== downloads macroeconomic data from fred and world bank apis. requires: fredap	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/index.md	0	economic data fetcher ===================== downloads macroeconomic data from fred and world bank apis. requires: fredap	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/SKILL.md	0	economic data fetcher ===================== downloads macroeconomic data from fred and world bank apis. requires: fredap	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/index.md	0	economic data fetcher ===================== downloads macroeconomic data from fred and world bank apis. requires: fredap	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/SKILL.md	0	economic data fetcher ===================== downloads macroeconomic data from fred and world bank apis. requires: fredap	STRING
HIGH	…ills/67-econfin-workflow-toolkit/data-fetcher/SKILL.md	0	fetch time series data from fred. parameters ---------- series_ids : list of str fred series ids (e.g., ['gdp', 'unrate'	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/index.md	0	fetch time series data from fred. parameters ---------- series_ids : list of str fred series ids (e.g., ['gdp', 'unrate'	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/SKILL.md	0	fetch time series data from fred. parameters ---------- series_ids : list of str fred series ids (e.g., ['gdp', 'unrate'	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/index.md	0	fetch time series data from fred. parameters ---------- series_ids : list of str fred series ids (e.g., ['gdp', 'unrate'	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/SKILL.md	0	fetch time series data from fred. parameters ---------- series_ids : list of str fred series ids (e.g., ['gdp', 'unrate'	STRING
HIGH	…ills/67-econfin-workflow-toolkit/data-fetcher/SKILL.md	0	fetch indicator data from world bank. parameters ---------- indicators : dict dict mapping indicator codes to names e.g.	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/index.md	0	fetch indicator data from world bank. parameters ---------- indicators : dict dict mapping indicator codes to names e.g.	STRING
HIGH	…e-econ-ai-stuff/_skills/data/api-data-fetcher/SKILL.md	0	fetch indicator data from world bank. parameters ---------- indicators : dict dict mapping indicator codes to names e.g.	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/index.md	0	fetch indicator data from world bank. parameters ---------- indicators : dict dict mapping indicator codes to names e.g.	STRING
HIGH	…ude-code-skills/_skills/data/api-data-fetcher/SKILL.md	0	fetch indicator data from world bank. parameters ---------- indicators : dict dict mapping indicator codes to names e.g.	STRING
HIGH	…toolkit/stata/references/external-tools-integration.md	0	use prepared_data, clear regress log_income education experience estimates store model1 esttab model1 using results.tex,	STRING
HIGH	…/skills/stata/references/external-tools-integration.md	0	use prepared_data, clear regress log_income education experience estimates store model1 esttab model1 using results.tex,	STRING
HIGH	…/skills/stata/references/external-tools-integration.md	0	use prepared_data, clear regress log_income education experience estimates store model1 esttab model1 using results.tex,	STRING
HIGH	…code-research-starter/dot-claude/hooks/log-reminder.py	0	session log reminder hook for claude code a stop hook that tracks how many responses have passed since the session log w	STRING
HIGH	…aude-code-my-workflow/dot-claude/hooks/log-reminder.py	0	session log reminder hook for claude code a stop hook that tracks how many responses have passed since the session log w	STRING
HIGH	…-replicate-agent-demo/dot-claude/hooks/log-reminder.py	0	session log reminder hook for claude code a stop hook that tracks how many responses have passed since the session log w	STRING
HIGH	…code-research-starter/dot-claude/hooks/log-reminder.py	0	get project directory from stdin json or environment.	STRING
HIGH	…aude-code-my-workflow/dot-claude/hooks/log-reminder.py	0	get project directory from stdin json or environment.	STRING
HIGH	…-replicate-agent-demo/dot-claude/hooks/log-reminder.py	0	get project directory from stdin json or environment.	STRING
HIGH	…code-research-starter/dot-claude/hooks/log-reminder.py	0	find the most recently modified .md file in session_logs/.	STRING
HIGH	…aude-code-my-workflow/dot-claude/hooks/log-reminder.py	0	find the most recently modified .md file in session_logs/.	STRING
HIGH	…-replicate-agent-demo/dot-claude/hooks/log-reminder.py	0	find the most recently modified .md file in session_logs/.	STRING
HIGH	…e-my-workflow/dot-claude/hooks/post-compact-restore.py	0	post-compact context restoration hook fires after compaction (sessionstart with type="compact") to restore context. read	STRING
HIGH	…-social-science-research/hooks/post-compact-restore.py	0	post-compact context restoration hook fires after compaction (sessionstart with type="compact") to restore context. read	STRING
HIGH	…88-clo-author/dot-claude/hooks/post-compact-restore.py	0	post-compact context restoration hook fires after compaction (sessionstart with type="compact") to restore context. read	STRING
HIGH	…e-my-workflow/dot-claude/hooks/post-compact-restore.py	0	find the most recent plan file and extract its status.	STRING
HIGH	…-social-science-research/hooks/post-compact-restore.py	0	find the most recent plan file and extract its status.	STRING
HIGH	…88-clo-author/dot-claude/hooks/post-compact-restore.py	0	find the most recent plan file and extract its status.	STRING
HIGH	…references/knowledge/time-series/birdclef-plus-2025.md	0	提取 mel-spectrogram args: waveform: (num_samples,) 或 (batch, num_samples) returns: mel_spec: (n_mels, time) 或 (batch, n_m	STRING
HIGH	…rner/references/knowledge/time-series/birdclef-2023.md	0	提取 mel-spectrogram args: waveform: (num_samples,) 或 (batch, num_samples) returns: mel_spec: (n_mels, time) 或 (batch, n_m	STRING
HIGH	…e-learner/references/knowledge/.archive/time-series.md	0	提取 mel-spectrogram args: waveform: (num_samples,) 或 (batch, num_samples) returns: mel_spec: (n_mels, time) 或 (batch, n_m	STRING
HIGH	…references/knowledge/time-series/birdclef-plus-2025.md	0	提取固定长度的 mel-spectrogram（用于 5 秒音频） args: waveform: (num_samples,) target_length: 目标时间维度 returns: mel_spec: (n_mels, targe	STRING
HIGH	…rner/references/knowledge/time-series/birdclef-2023.md	0	提取固定长度的 mel-spectrogram（用于 5 秒音频） args: waveform: (num_samples,) target_length: 目标时间维度 returns: mel_spec: (n_mels, targe	STRING
HIGH	…e-learner/references/knowledge/.archive/time-series.md	0	提取固定长度的 mel-spectrogram（用于 5 秒音频） args: waveform: (num_samples,) target_length: 目标时间维度 returns: mel_spec: (n_mels, targe	STRING
HIGH	…ls/skills/latex-thesis-zh/scripts/online_bib_verify.py	0	online bibliography verification via crossref and semantic scholar apis. verifies bibliography entries against online da	STRING
HIGH	…skills/skills/typst-paper/scripts/online_bib_verify.py	0	online bibliography verification via crossref and semantic scholar apis. verifies bibliography entries against online da	STRING
HIGH	…lls/skills/latex-paper-en/scripts/online_bib_verify.py	0	online bibliography verification via crossref and semantic scholar apis. verifies bibliography entries against online da	STRING
HIGH	…ls/skills/latex-thesis-zh/scripts/online_bib_verify.py	0	verify bibliography entries via crossref and semantic scholar apis.	STRING
HIGH	…skills/skills/typst-paper/scripts/online_bib_verify.py	0	verify bibliography entries via crossref and semantic scholar apis.	STRING
HIGH	…lls/skills/latex-paper-en/scripts/online_bib_verify.py	0	verify bibliography entries via crossref and semantic scholar apis.	STRING
HIGH	…ls/skills/latex-thesis-zh/scripts/online_bib_verify.py	0	search for a paper by title via semantic scholar api.	STRING
HIGH	…skills/skills/typst-paper/scripts/online_bib_verify.py	0	search for a paper by title via semantic scholar api.	STRING
HIGH	…lls/skills/latex-paper-en/scripts/online_bib_verify.py	0	search for a paper by title via semantic scholar api.	STRING
HIGH	…ls/skills/latex-thesis-zh/scripts/online_bib_verify.py	0	verify a single bibliography entry. strategy: doi verification first, fallback to title search. args: entry: dict with k	STRING
HIGH	…skills/skills/typst-paper/scripts/online_bib_verify.py	0	verify a single bibliography entry. strategy: doi verification first, fallback to title search. args: entry: dict with k	STRING
HIGH	…lls/skills/latex-paper-en/scripts/online_bib_verify.py	0	verify a single bibliography entry. strategy: doi verification first, fallback to title search. args: entry: dict with k	STRING
HIGH	…ls/skills/latex-thesis-zh/scripts/online_bib_verify.py	0	compare bib entry metadata against api-returned metadata.	STRING
HIGH	…skills/skills/typst-paper/scripts/online_bib_verify.py	0	compare bib entry metadata against api-returned metadata.	STRING
HIGH	…lls/skills/latex-paper-en/scripts/online_bib_verify.py	0	compare bib entry metadata against api-returned metadata.	STRING
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Excessive Try-Catch Wrapping295 hits · 304 pts

Severity	File	Line	Snippet	Context
LOW	demo-notebooks/statsPAI_pipeline_v2.py	96	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	317	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	411	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	456	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	549	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	554	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	620	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	626	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	694	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	703	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	747	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	115	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	380	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	382	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	430	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	440	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	446	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	451	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	457	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	577	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	630	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	638	except Exception as exc:	CODE
LOW⚡	demo-notebooks/statsPAI_pipeline_5.2.py	766	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	54	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	66	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	76	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	93	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	198	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	200	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	216	except Exception:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	298	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	359	except Exception as e:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	404	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	417	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	480	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	492	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	503	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	550	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	564	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	654	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	693	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	706	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	717	except Exception as exc:	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	802	except Exception as exc:	CODE
LOW⚡	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	268	except Exception as e:	CODE
LOW⚡	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	277	except Exception as e2:	CODE
LOW⚡	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	300	except Exception as e:	CODE
LOW⚡	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	327	except Exception as e:	CODE
LOW⚡	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	341	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	369	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	456	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	471	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	486	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	499	except Exception as e:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	541	except Exception:	CODE
LOW	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	564	except Exception as e:	CODE
LOW	eval-harness/run_evals.py	407	except Exception as exc: # network/parse failure must not crash the run	CODE
LOW⚡	…ins/empirical-analysis-python/skills/pipeline/SKILL.md	1378	except Exception:	CODE
LOW	…sis-python/skills/pipeline/references/06-robustness.md	212	except Exception as e:	CODE
LOW	…o-StatsPAI-skill/card_returns_to_schooling_pipeline.py	205	except Exception:	CODE
235 more matches not shown…

Unused Imports311 hits · 302 pts

Severity	File	Line	Context
LOW	benchmark/check_benchmark.py	19	CODE
LOW	benchmark/reference_pipeline.py	9	CODE
LOW	benchmark/lib/structural.py	61	CODE
LOW	benchmark/lib/synth.py	16	CODE
LOW	benchmark/lib/badcontrol.py	27	CODE
LOW	benchmark/lib/oaxaca.py	29	CODE
LOW	benchmark/lib/spillover.py	53	CODE
LOW	benchmark/lib/eventstudy.py	14	CODE
LOW	benchmark/lib/survival.py	12	CODE
LOW	benchmark/lib/panelfe.py	12	CODE
LOW	benchmark/lib/rdd.py	22	CODE
LOW	benchmark/lib/card.py	9	CODE
LOW	benchmark/lib/bunching.py	28	CODE
LOW	benchmark/lib/bunching.py	31	CODE
LOW	benchmark/lib/cate.py	18	CODE
LOW	benchmark/lib/qte.py	17	CODE
LOW	benchmark/lib/mediation.py	23	CODE
LOW	benchmark/lib/bartik.py	18	CODE
LOW	benchmark/lib/bayesian.py	11	CODE
LOW	benchmark/lib/dml.py	16	CODE
LOW	benchmark/lib/lalonde.py	9	CODE
LOW	benchmark/lib/simdid.py	11	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	34	CODE
LOW	demo-notebooks/statsPAI_pipeline_v2.py	153	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	18	CODE
LOW	demo-notebooks/statsPAI_pipeline_5.2.py	161	CODE
LOW	demo-notebooks/manuscript_docx_demo.py	39	CODE
LOW	demo-notebooks/card-krueger-1994/replicate_ck1994.py	37	CODE
LOW	demo-notebooks/nsw-lalonde-1986/replicate_nsw.py	33	CODE
LOW	…books/_stata_lalonde_outputs/_pregenerate_artifacts.py	17	CODE
LOW	demo-notebooks/card-1995-iv/replicate_card1995.py	48	CODE
LOW	demo-notebooks/_python_pipeline_outputs/_runner_v2.py	10	CODE
LOW	demo-notebooks/_python_pipeline_outputs/_runner_v2.py	21	CODE
LOW	eval-harness/run_evals.py	36	CODE
LOW	eval-harness/lib/checks.py	15	CODE
LOW	tests/test_scan_collections.py	18	CODE
LOW	tests/test_skillopt_gates.py	3	CODE
LOW	tests/test_validate_workflows.py	3	CODE
LOW	tests/test_split.py	3	CODE
LOW	tests/test_check_links.py	3	CODE
LOW	tests/test_structural_benchmark.py	12	CODE
LOW	tests/test_eval_scenarios.py	3	CODE
LOW	tests/test_quickstart.py	14	CODE
LOW	tests/test_eval_selftest.py	16	CODE
LOW	tests/test_generator_freshness.py	13	CODE
LOW	tests/test_nsw_replication.py	14	CODE
LOW	tests/test_spillover_benchmark.py	16	CODE
LOW	tests/test_doctor.py	9	CODE
LOW	tests/test_repo_tools.py	3	CODE
LOW	tests/test_readme_stats.py	3	CODE
LOW	tests/test_build_catalog.py	18	CODE
LOW	tests/test_build_catalog.py	25	CODE
LOW	tests/test_requirements.py	17	CODE
LOW	tests/test_routing.py	3	CODE
LOW	tests/test_card1995_replication.py	15	CODE
LOW	tests/test_validate_repo.py	19	CODE
LOW	tests/test_hygiene.py	3	CODE
LOW	tests/test_toml_compat.py	3	CODE
LOW	tests/test_benchmark.py	3	CODE
LOW	tests/test_external_scoreboard.py	14	CODE
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Modern AI Meta-Vocabulary68 hits · 188 pts

Severity	File	Line	Snippet	Context
MEDIUM	INSTALL.md	158	aers-score init ./my-run # scaffold candidates with the right fields	CODE
MEDIUM	README-en.md	188	- [Multi-agent systems · MCP servers · platforms · learning](#multi-agent-systems--mcp-servers--platforms--learning)	CODE
MEDIUM	tools/tools.json	6291	"url": "https://github.com/K-Dense-AI/agentic-data-scientist",	CODE
MEDIUM	tools/CATALOG.md	279	\| [Agentic Data Scientist](https://github.com/K-Dense-AI/agentic-data-scientist) \| Python \| MIT \| 🟢 active · 2026-05 \| A	CODE
MEDIUM	tools/CATALOG.md	287	\| [AutoMind](https://github.com/innovatingAI/AutoMind) \| Python \| MIT \| 🟢 active · 2025-10 \| An adaptive, knowledge-grou	CODE
MEDIUM	tools/CATALOG.md	301	\| [DeepAnalyze](https://github.com/ruc-datalab/DeepAnalyze) \| Python \| MIT \| 🟢 active · 2026-03 \| An agentic LLM (DeepAn	CODE
MEDIUM	tools/CATALOG.md	306	\| [Jupyter AI](https://github.com/jupyterlab/jupyter-ai) \| Python \| BSD-3-Clause \| 🟢 active · 2026-04 \| A JupyterLab ext	CODE
MEDIUM	tools/CATALOG.md	326	\| [The AI Scientist-v2](https://github.com/SakanaAI/AI-Scientist-v2) \| Python \| AI Scientist Source Code License v1.0 (c	CODE
MEDIUM⚡	tests/test_aers_score.py	124	# A scaffold that omits a graded field sends the user into a required	COMMENT
MEDIUM	docs/BENCHMARK_SCOREBOARD.md	42	aers-score init ./my-run # scaffold candidates with the exact fields	CODE
MEDIUM	docs/SKILL_CATALOG.md	33	\| 10 \| [`06-fuhaoda-stats-paper-writing`](../skills/06-fuhaoda-stats-paper-writing/) \| 1 \| MIT \| [source](https://github	CODE
MEDIUM	docs/SKILL_CATALOG.md	50	\| 27 \| [`23-Learning-Bayesian-Statistics-baygent-skills`](../skills/23-Learning-Bayesian-Statistics-baygent-skills/) \| 2	CODE
MEDIUM	aers_score/README.md	45	aers-score init ./my-run # scaffold candidates with the exact fields	CODE
MEDIUM	scripts/build-benchmark-scoreboard.py	237	"aers-score init ./my-run # scaffold candidates with the exact fields\n"	CODE
MEDIUM	skills/26-Data-Wise-scholar/CLAUDE.md	79	│ │ ├── demo-templates/ # Demo course scaffolding templates	CODE
MEDIUM	…n-Statistics-baygent-skills/causal-inference/README.md	87	└── reporting.md # Causal language guardrails, report templates	CODE
MEDIUM	…aygent-skills/causal-inference/references/reporting.md	6	2. [Causal language guardrails](#causal-language-guardrails)	CODE
MEDIUM	…aygent-skills/causal-inference/references/reporting.md	95	If a refutation test fails, downgrade the causal language accordingly — see [Causal language guardrails](#causal-languag	CODE
MEDIUM	…aygent-skills/causal-inference/references/reporting.md	119	## Causal language guardrails	COMMENT
MEDIUM	…ills/research/methodology/research-town-guide/SKILL.md	151	# Rank ideas by multi-agent consensus	COMMENT
MEDIUM	…/research/deep-research/open-researcher-guide/SKILL.md	36	# SQ1: What types of knowledge conflicts occur in RAG?	COMMENT
MEDIUM⚡	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	13	# RAG Methodology Guide	COMMENT
MEDIUM⚡	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	17	## What Is RAG?	COMMENT
MEDIUM⚡	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	26	### RAG Pipeline Architecture	COMMENT
MEDIUM	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	150	# Initialize embedding model (local, free)	COMMENT
MEDIUM	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	299	# Using RAGAS for automated RAG evaluation	COMMENT
MEDIUM	…s/tools/knowledge-graph/rag-methodology-guide/SKILL.md	318	## Best Practices for Academic RAG	COMMENT
MEDIUM⚡	…/knowledge-graph/knowledge-graph-construction/SKILL.md	248	## Knowledge Graph + RAG Integration	COMMENT
MEDIUM	…ns/skills/tools/document/pdf-extraction-guide/SKILL.md	205	## Document Chunking for RAG	COMMENT
MEDIUM	…ng-p-hacking-skills/skills/04-framing-attacks/SKILL.md	6	# Framings that move statistical guardrails	COMMENT
MEDIUM	skills/25-HosungYou-Diverga/agents/i0.md	83	# Stage 6: RAG Building	STRING
MEDIUM	skills/25-HosungYou-Diverga/agents/i3.md	73	# Stage 5: RAG Build	COMMENT
MEDIUM	skills/25-HosungYou-Diverga/skills/i0/SKILL.md	152	# Stage 6: RAG Building	STRING
MEDIUM	…osungYou-Diverga/skills/universal-ma-codebook/SKILL.md	362	# After Stage 5 (RAG building)	COMMENT
MEDIUM	…osungYou-Diverga/skills/universal-ma-codebook/SKILL.md	363	# RAG query integration	COMMENT
MEDIUM	skills/25-HosungYou-Diverga/skills/i3/SKILL.md	131	# Stage 5: RAG Build	COMMENT
MEDIUM	…27-dariia-m-my_claude_skills/academic_writing/SKILL.md	14	### 0.1 Examples are scaffolding, not copy-paste	COMMENT
MEDIUM	…27-dariia-m-my_claude_skills/academic_writing/SKILL.md	183	### 6.3 Abstract drafting template (example scaffold—rewrite)	COMMENT
MEDIUM	…27-dariia-m-my_claude_skills/academic_writing/SKILL.md	245	### 8.3 Cluster scaffold (rewrite; provide alternatives)	COMMENT
MEDIUM	…27-dariia-m-my_claude_skills/academic_writing/SKILL.md	351	### 13.2 Conclusion scaffold (rewrite; provide alternatives)	COMMENT
MEDIUM	…27-dariia-m-my_claude_skills/academic_writing/SKILL.md	387	### 15.3 Variable-definition scaffold (rewrite; provide alternatives)	COMMENT
MEDIUM	…ar/skills/plugin-structure/examples/advanced-plugin.md	225	### agents/orchestration/deployment-orchestrator.md	COMMENT
MEDIUM	…-Imbad0202-academic-research-skills/README-original.md	189	Use these skills in [Claude Cowork](https://claude.com/product/cowork) — Claude Desktop's agentic workspace for knowledg	CODE
MEDIUM	skills/05-kthorn-research-superpower/README-original.md	81	│ ├── answering-research-questions/ # Main orchestration	CODE
MEDIUM	…rycewang-aer-skills/examples/end-to-end-walkthrough.md	164	# scaffold the replication package	COMMENT
MEDIUM	…ls/50-brycewang-aer-skills/scripts/verify_citations.py	531	# automated claim-support / anti-hallucination check --- a citation that points	COMMENT
MEDIUM⚡	skills/50-brycewang-aer-skills/templates/r/07_figures.R	3	# Publication-ready figure scaffold.	COMMENT
MEDIUM⚡	…ls/50-brycewang-aer-skills/templates/r/04_robustness.R	3	# Referee-anticipating robustness scaffold.	COMMENT
MEDIUM⚡	…50-brycewang-aer-skills/templates/r/05_heterogeneity.R	3	# Heterogeneity and mechanism scaffold.	COMMENT
MEDIUM⚡	…/50-brycewang-aer-skills/templates/r/02_descriptives.R	3	# Summary-statistics scaffold.	COMMENT
MEDIUM	…pen-science-skills/skills/replication-package/SKILL.md	62	### Step 3. Decide between scaffold and audit	COMMENT
MEDIUM	skills/13-scunning1975-MixtapeTools/README-original.md	216	│ └── newproject/ # Documentation for the new-project scaffold skill	CODE
MEDIUM	skills/13-scunning1975-MixtapeTools/README-original.md	229	│ └── newproject/ # Skill: scaffold new research projects	CODE
MEDIUM	…ills/06-fuhaoda-stats-paper-writing/README-original.md	114	### 6) Book manuscript scaffold	COMMENT
MEDIUM	…s/06-fuhaoda-stats-paper-writing/stat-writing/SKILL.md	157	### Workflow F - Book manuscript scaffolding	COMMENT
MEDIUM	…ent-tools/literature-review-tools/reference/catalog.md	49	\| ⭐ [AI-Scientist](https://github.com/SakanaAI/AI-Scientist) \| ~14.3k \| Sakana AI, end-to-end automated discovery (lit→e	CODE
MEDIUM	…ent-tools/literature-review-tools/reference/catalog.md	56	## 📚 Literature Q&A & RAG	COMMENT
MEDIUM	…ent-tools/literature-review-tools/reference/catalog.md	133	\| [lmms-lab-writer](https://github.com/EvolvingLMMs-Lab/lmms-lab-writer) \| ~0.3k \| Local-first agentic LaTeX writing for	CODE
MEDIUM	…motions-research-methods/skills/research-init/SKILL.md	17	## How to scaffold a project	COMMENT
MEDIUM	…chestra-Research-AI-Research-SKILLs/README-original.md	274	### 🔍 RAG (5 skills)	COMMENT
8 more matches not shown…

Over-Commented Block177 hits · 157 pts

Severity	File	Line	Snippet	Context
LOW	requirements.txt	1	# Pinned scientific stack for the CI / Paper-WorkFlow demo gate.	COMMENT
LOW	requirements.txt	21	# the quality matrix installs nothing (every gate it runs is stdlib-only).	COMMENT
LOW	pyproject.toml	1	# Packaging for `aers-score` — the CLI front end to the AERS numeric benchmark.	COMMENT
LOW	demo-notebooks/statsPAI_pipeline_v2.py	1	# %% [markdown]	COMMENT
LOW	demo-notebooks/statsPAI_pipeline_v2.py	21	# \| 横截面 (无 time/id) \| 单期 \| DID, 事件研究, SCM \| Selection on observables \|	COMMENT
LOW	demo-notebooks/statsPAI_pipeline_v2.py	241	# ```	COMMENT
LOW	demo-notebooks/statsPAI_pipeline_v2.py	861	# tableA1_robustness.{docx,xlsx,tex}	COMMENT
LOW	…-python/skills/pipeline/references/01-data-cleaning.md	201	# - Keep the most recent record: df = df.sort_values("timestamp").drop_duplicates(["worker_id","year"], keep="la	COMMENT
LOW	plugins/empirical-analysis-r/skills/pipeline/SKILL.md	1701	honest_out <- createSensitivityResults(betahat = es$coefficients,	COMMENT
LOW	plugins/empirical-analysis-r/skills/pipeline/SKILL.md	1741		COMMENT
LOW	agents/anthropic.yaml	1	# Anthropic Claude Code / Claude API entry point for the AERS catalog.	COMMENT
LOW	agents/cursor.yaml	1	# Cursor IDE entry point for the AERS catalog.	COMMENT
LOW	agents/aider.yaml	1	# Aider CLI entry point for the AERS catalog.	COMMENT
LOW	agents/codebuddy.yaml	1	# Tencent CodeBuddy entry point for the AERS catalog.	COMMENT
LOW	scripts/build-provenance.py	21	DEFAULT_MARKDOWN = ROOT / "docs" / "LICENSE_AUDIT.md"	COMMENT
LOW	scripts/build-provenance.py	241	# snapshot was taken, so github.com/voidborne-d/humanize-chinese now	COMMENT
LOW	scripts/build-catalog.py	161	for filename in filenames:	COMMENT
LOW	scripts/sync-aer-skills.sh	1	#!/usr/bin/env bash	COMMENT
LOW	scripts/sync-statspai-skill.sh	1	#!/usr/bin/env bash	COMMENT
LOW	.github/workflows/refresh-star-history.yml	1	name: Refresh star-history chart	COMMENT
LOW	…AI-claude-scientific-writer/literature-review/SKILL.md	521	--format markdown \	COMMENT
LOW	…ow-toolkit/agent-browser/templates/capture-workflow.sh	1	#!/bin/bash	COMMENT
LOW	…low-toolkit/agent-browser/templates/form-automation.sh	1	#!/bin/bash	COMMENT
LOW	…low-toolkit/agent-browser/templates/form-automation.sh	21	agent-browser open "$FORM_URL"	COMMENT
LOW	…olkit/agent-browser/templates/authenticated-session.sh	1	#!/bin/bash	COMMENT
LOW	…olkit/agent-browser/templates/authenticated-session.sh	81	# # Fill credentials (update refs to match your form)	COMMENT
LOW	…econfin-workflow-toolkit/stata/packages/event-study.md	101		COMMENT
LOW	…67-econfin-workflow-toolkit/stata/packages/psmatch2.md	81	// After matching, psmatch2 creates:	COMMENT
LOW	…ly-superpapers/skills/compile-latex/scripts/compile.sh	1	#!/usr/bin/env bash	COMMENT
LOW	…ls/63-tondevrel-scientific-agent-skills/dowhy/SKILL.md	921	# T and Y are INDEPENDENT — no causal relationship.	COMMENT
LOW	…ls/63-tondevrel-scientific-agent-skills/dowhy/SKILL.md	961	# When DoWhy says "effect not identifiable" — it means:	COMMENT
LOW	…e-scholar/skills/research/sensitivity-analyst/SKILL.md	41		COMMENT
LOW	…skills/implementation/computational-inference/SKILL.md	121	#' Importance Sampling Estimator	COMMENT
LOW	…skills/implementation/computational-inference/SKILL.md	461	### ABC for Mediation	COMMENT
LOW	…e-scholar/skills/writing/methods-communicator/SKILL.md	441	#'	COMMENT
LOW	…e/skills/workflows-review/references/project-config.md	81	# Estimation language (auto-detected)	COMMENT
LOW	…ce/skills/causal-inference/references/staggered-did.md	41	# result <- feols(	COMMENT
LOW	…kills/causal-inference/references/synthetic-control.md	81	```	COMMENT
LOW	…lls/research/automation/ai-scientist-v2-guide/SKILL.md	181	# Compile to PDF	COMMENT
LOW	…ls/knowledge-graph/notero-zotero-notion-guide/SKILL.md	61	# - Share your database with the integration	COMMENT
LOW	…ugins/skills/domains/biomedical/clawbio-guide/SKILL.md	41	\| phylogenetics \| IQ-TREE + RAxML \| Phylogenetic tree construction \|	COMMENT
LOW	…ugins/skills/domains/biomedical/clawbio-guide/SKILL.md	61	# 7. Pathway enrichment (GSEA)	COMMENT
LOW	…s/analysis/wrangling/streamline-analyst-guide/SKILL.md	61		COMMENT
LOW	…s/analysis/wrangling/streamline-analyst-guide/SKILL.md	81	# - Statistical tests (t-test, ANOVA, chi-square, Mann-Whitney)	COMMENT
LOW	…literature/discovery/literature-mapping-guide/SKILL.md	61		COMMENT
LOW	…ls/writing/citation/academic-citation-manager/SKILL.md	41	# Example	COMMENT
LOW	…ills/writing/templates/scientific-article-pdf/SKILL.md	41	# Key file: acmart.cls (supports all ACM formats)	COMMENT
LOW	…l-analysis-skill_Python/references/01-data-cleaning.md	201	# - Keep the most recent record: df = df.sort_values("timestamp").drop_duplicates(["worker_id","year"], keep="la	COMMENT
LOW	skills/25-HosungYou-Diverga/skills/memory/SKILL.md	681	```python	COMMENT
LOW	…s/02-luwill-research-skills/research-proposal/SKILL.md	221	### 1.2 Problem Statement	COMMENT
LOW	…luwill-research-skills/medical-imaging-review/SKILL.md	101		COMMENT
LOW	…ills/paper_verification/replication-script-template.md	141		COMMENT
LOW	…claude_skills/event-studies/diagnostics-and-testing.md	341	---	COMMENT
LOW	…earch-starter/dot-claude/skills/data-analysis/SKILL.md	41	- Export figures as `.pdf` and `.png`	COMMENT
LOW	…tarter/dot-claude/skills/stata/packages/event-study.md	101		COMMENT
LOW	…h-starter/dot-claude/skills/stata/packages/psmatch2.md	61	// After matching, psmatch2 creates:	COMMENT
LOW	…kills/architecture-design/examples/pipeline_example.sh	1	#!/bin/bash	COMMENT
LOW	…Dawn-claude-scholar/skills/uv-package-manager/SKILL.md	341	```	COMMENT
LOW	…rner/references/knowledge/time-series/birdclef-2024.md	1001		COMMENT
LOW	…rner/references/knowledge/time-series/birdclef-2024.md	2481	"""	COMMENT
117 more matches not shown…

Deep Nesting163 hits · 153 pts

Severity	File	Line	Context
LOW	benchmark/check_benchmark.py	223	CODE
LOW	benchmark/check_benchmark.py	603	CODE
LOW	eval-harness/run_evals.py	136	CODE
LOW	eval-harness/run_evals.py	386	CODE
LOW	eval-harness/run_evals.py	637	CODE
LOW	tests/test_aers_score.py	133	CODE
LOW	…o-StatsPAI-skill/card_returns_to_schooling_pipeline.py	62	CODE
LOW	aers_score/cli.py	285	CODE
LOW	scripts/check-mirror-sync.py	65	CODE
LOW	scripts/check-routing.py	68	CODE
LOW	scripts/scan-collections.py	345	CODE
LOW	scripts/build-external-scoreboard.py	277	CODE
LOW	scripts/build-tools-catalog.py	165	CODE
LOW	scripts/build-release-notes.py	255	CODE
LOW	scripts/validate-repo.py	166	CODE
LOW	scripts/toml_compat.py	61	CODE
LOW	scripts/toml_compat.py	130	CODE
LOW	scripts/toml_compat.py	166	CODE
LOW	scripts/toml_compat.py	221	CODE
LOW	scripts/quickstart.py	54	CODE
LOW	scripts/build-coverage-map.py	188	CODE
LOW	…orkflow-toolkit/journal-digest/scripts/fetch_papers.py	90	CODE
LOW	…orkflow-toolkit/journal-digest/scripts/fetch_papers.py	160	CODE
LOW	…orkflow-toolkit/journal-digest/scripts/fetch_papers.py	232	CODE
LOW	…s/67-econfin-workflow-toolkit/md-to-docx/fix_tables.py	102	CODE
LOW	…nfin-workflow-toolkit/md-to-docx/convert_md_to_docx.py	80	CODE
LOW	…nfin-workflow-toolkit/md-to-docx/convert_md_to_docx.py	182	CODE
LOW	…nfin-workflow-toolkit/md-to-docx/convert_md_to_docx.py	301	CODE
LOW	…onfin-workflow-toolkit/md-to-docx/fix_heading_fonts.py	14	CODE
LOW	…w-toolkit/skill-creator/eval-viewer/generate_review.py	85	CODE
LOW	…w-toolkit/skill-creator/eval-viewer/generate_review.py	149	CODE
LOW	…w-toolkit/skill-creator/eval-viewer/generate_review.py	288	CODE
LOW	…fin-workflow-toolkit/skill-creator/scripts/run_eval.py	35	CODE
LOW	…orkflow-toolkit/skill-creator/scripts/package_skill.py	42	CODE
LOW	…w-toolkit/skill-creator/scripts/improve_description.py	50	CODE
LOW	…w-toolkit/skill-creator/scripts/aggregate_benchmark.py	67	CODE
LOW	…kflow-toolkit/skill-creator/scripts/generate_report.py	16	CODE
LOW	…confin-workflow-toolkit/skill-creator/scripts/utils.py	7	CODE
LOW	…w-toolkit/paper-submission/scripts/extract_journals.py	19	CODE
LOW	…w-toolkit/paper-submission/scripts/extract_journals.py	135	CODE
LOW	…lkit/chinese-quote-converter/scripts/convert_quotes.py	52	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	178	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	237	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	302	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	347	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	445	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	554	CODE
LOW	…ude-skill-citation-checker/scripts/citation_checker.py	183	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/grid.py	591	CODE
LOW	…3-brycewang-p-hacking-skills/scripts/phack/polyglot.py	63	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/core.py	147	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/core.py	220	CODE
LOW	…s/73-brycewang-p-hacking-skills/scripts/phack/bench.py	70	CODE
LOW	…-brycewang-p-hacking-skills/scripts/phack/init_card.py	43	CODE
LOW	…-brycewang-p-hacking-skills/scripts/phack/init_card.py	63	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	117	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	230	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	449	CODE
LOW	…brycewang-p-hacking-skills/scripts/phack/procedures.py	182	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/verify.py	40	CODE
103 more matches not shown…

Empty Error Handlers30 hits · 150 pts

Severity	File	Line	Snippet	Context
HIGH	demo-notebooks/statsPAI_pipeline_v2.py	703	except Exception:	CODE
HIGH	demo-notebooks/statsPAI_pipeline_5.2.py	66	except Exception:	CODE
HIGH	demo-notebooks/statsPAI_pipeline_5.2.py	76	except Exception:	CODE
HIGH	demo-notebooks/statsPAI_pipeline_5.2.py	198	except Exception:	CODE
HIGH	…ebooks/_statspai_pipeline_outputs_5.2/full_analysis.py	541	except Exception:	CODE
HIGH	scripts/build-star-history.py	86	except (OSError, subprocess.SubprocessError):	CODE
HIGH	…orkflow-toolkit/journal-digest/scripts/fetch_papers.py	308	except Exception:	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	303	except subprocess.TimeoutExpired:	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	231	except (json.JSONDecodeError, OSError, KeyError):	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	428	except (json.JSONDecodeError, OSError):	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	97	except (json.JSONDecodeError, OSError):	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	135	except (json.JSONDecodeError, OSError):	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	111	except OSError:	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	299	except (ProcessLookupError, ValueError):	CODE
HIGH	…w-toolkit/skill-creator/eval-viewer/generate_review.py	340	except (json.JSONDecodeError, OSError):	CODE
HIGH	…w-toolkit/skill-creator/scripts/aggregate_benchmark.py	146	except json.JSONDecodeError:	CODE
HIGH	…w-toolkit/paper-submission/scripts/extract_journals.py	111	except ValueError:	CODE
HIGH	…/73-brycewang-p-hacking-skills/scripts/phack/rundir.py	84	except OSError:	CODE
HIGH	…laude-code-my-workflow/dot-claude/hooks/pre-compact.py	143	except IOError:	CODE
HIGH	…e-code-my-workflow/dot-claude/hooks/verify-reminder.py	127	except IOError:	CODE
HIGH	…e-code-my-workflow/dot-claude/hooks/context-monitor.py	72	except IOError:	CODE
HIGH	skills/50-brycewang-aer-skills/scripts/validate_repo.py	530	except ImportError:	CODE
HIGH	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1728	except Exception:	CODE
HIGH	…ting-skills/skills/paper-audit/scripts/scholar_eval.py	260	except Exception:	CODE
HIGH	…-skills/skills/paper-audit/scripts/report_generator.py	1020	except Exception:	CODE
HIGH	…-skills/skills/paper-audit/scripts/report_generator.py	1036	except Exception:	CODE
HIGH	…skills/skills/paper-audit/scripts/literature_search.py	283	except (ImportError, TypeError):	CODE
HIGH	…skills/skills/paper-audit/scripts/literature_search.py	193	except ET.ParseError:	CODE
HIGH	…x-Studios-social-science-research/hooks/pre-compact.py	143	except IOError:	CODE
HIGH	…hsantanna88-clo-author/dot-claude/hooks/pre-compact.py	141	except IOError:	CODE

Magic Placeholder Names25 hits · 110 pts

Severity	File	Line	Snippet	Context
HIGH	skills/42-wanshuiyin-ARIS/README-original.md	918	vastai set api-key YOUR_API_KEY	CODE
HIGH	skills/42-wanshuiyin-ARIS/skills/vast-gpu/SKILL.md	21	vastai set api-key YOUR_API_KEY	CODE
HIGH	…2-wanshuiyin-ARIS/skills/auto-review-loop-llm/SKILL.md	35	"LLM_API_KEY": "your-api-key",	CODE
HIGH	…ARIS/skills/skills-codex/auto-review-loop-llm/SKILL.md	33	"LLM_API_KEY": "your-api-key",	CODE
HIGH	…w-toolkit/markitdown/references/document_conversion.md	28	docintel_key="YOUR-API-KEY"	CODE
HIGH	…toolkit/markitdown/references/advanced_integrations.md	34	docintel_key="YOUR-API-KEY"	CODE
HIGH	…toolkit/markitdown/references/advanced_integrations.md	237	os.environ['OPENAI_API_KEY'] = 'YOUR-API-KEY'	CODE
HIGH	…toolkit/markitdown/references/advanced_integrations.md	251	client = Anthropic(api_key="YOUR-API-KEY")	CODE
HIGH	…toolkit/stata/references/external-tools-integration.md	541	params = {'key': 'YOUR_API_KEY', 'format': 'json'}	STRING
HIGH	…toolkit/stata/references/external-tools-integration.md	590	key("your_api_key") params("limit=100,offset=0")	STRING
HIGH	…plugins/skills/domains/law/caselaw-access-api/SKILL.md	43	curl -H "Authorization: Token YOUR_API_KEY" \	CODE
HIGH	…h-plugins/skills/literature/search/pubmed-api/SKILL.md	28	&api_key=YOUR_API_KEY	CODE
HIGH	…gins/skills/literature/search/ieee-xplore-api/SKILL.md	32	apikey=YOUR_API_KEY&\	CODE
HIGH	…gins/skills/literature/search/ieee-xplore-api/SKILL.md	38	apikey=YOUR_API_KEY&\	CODE
HIGH	…gins/skills/literature/search/ieee-xplore-api/SKILL.md	84	apikey=YOUR_API_KEY&\	CODE
HIGH	…ch-plugins/skills/writing/citation/zotero-api/SKILL.md	34	curl -H "Zotero-API-Key: YOUR_API_KEY" "https://api.zotero.org/users/USER_ID/items"	CODE
HIGH	…/skills/stata/references/external-tools-integration.md	527	params = {'key': 'YOUR_API_KEY', 'format': 'json'}	STRING
HIGH	…/skills/stata/references/external-tools-integration.md	576	key("your_api_key") params("limit=100,offset=0")	STRING
HIGH	…/skills/stata/references/external-tools-integration.md	541	params = {'key': 'YOUR_API_KEY', 'format': 'json'}	STRING
HIGH	…/skills/stata/references/external-tools-integration.md	590	key("your_api_key") params("limit=100,offset=0")	STRING
HIGH	…/education-data-source-nhgis/references/data-access.md	114	-H "Authorization: YOUR_API_KEY"	CODE
HIGH	…/education-data-source-nhgis/references/data-access.md	131	api_key = "YOUR_API_KEY"	CODE
HIGH	…/education-data-source-nhgis/references/data-access.md	189	client = IpumsApiClient(api_key="YOUR_API_KEY")	CODE
HIGH	…/education-data-source-nhgis/references/data-access.md	240	client = IpumsApiClient("YOUR_API_KEY")	CODE
HIGH	…/education-data-source-nhgis/references/data-access.md	279	set_ipums_api_key("YOUR_API_KEY")	CODE

Cross-Language Confusion23 hits · 96 pts

Severity	File	Line	Snippet	Context
HIGH	tests/test_repo_tools.py	447	self.assertIn("make catalog && make check", text)	CODE
HIGH	scripts/build-tools-catalog.py	127	errors.append(f"{where}: mcp-server entries need a data_source field (may be null)")	CODE
HIGH⚡	…lls/73-brycewang-p-hacking-skills/tests/test_search.py	63	# honest p is uniform on a true null, so no single dataset can be held to a	COMMENT
HIGH	…3-brycewang-p-hacking-skills/scripts/phack/polyglot.py	22	cd run_stata && stata -b do run_specs.do # or Rscript run_specs.R, python run_specs.py	STRING
HIGH	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	6	null_calibration() -- re-run the identical search under an enforced null,	STRING
HIGH	…-brycewang-p-hacking-skills/scripts/phack/inference.py	193	def _p(obs, null, larger=True):	CODE
HIGH	…-brycewang-p-hacking-skills/scripts/phack/inference.py	194	null = null[np.isfinite(null)]	CODE
HIGH	…skills/citation-verification/scripts/format-checker.py	473	for key in sorted(undefined):	STRING
HIGH	…e-scholar/skills/webapp-testing/scripts/with_server.py	12	--server "cd backend && python server.py" --port 3000 \	STRING
HIGH	…e-scholar/skills/webapp-testing/scripts/with_server.py	13	--server "cd frontend && npm run dev" --port 5173 \	STRING
HIGH	…ization-inference-demo/randomization_inference_demo.py	8	t-test badly over-rejects a TRUE null, because the small arm's variance	STRING
HIGH⚡	…ization-inference-demo/randomization_inference_demo.py	132	labels = ["HC1 t-test\n(true null,\nheavy tails)",	CODE
HIGH⚡	…ization-inference-demo/randomization_inference_demo.py	133	"randomization\ntest (true null,\nheavy tails)",	CODE
HIGH⚡	…ization-inference-demo/randomization_inference_demo.py	134	"classical t\n(true null,\nwell-behaved)",	CODE
HIGH	…ization-inference-demo/randomization_inference_demo.py	198	"the\nrobust-SE t-test over-rejects a true null, while the Fisher "	CODE
HIGH	…aer-skills/examples/spec-curve-demo/spec_curve_demo.py	10	under the sharp null, not a single starred coefficient.	STRING
HIGH	…r-skills/examples/shift-share-demo/shift_share_demo.py	102	slope is exchangeable with the re-draws under the null, so the test has	STRING
HIGH	…g-aer-skills/examples/power-mde-demo/power_mde_demo.py	23	its nominal size under the null, and (4) the underpowered design exaggerates the	STRING
HIGH	…/50-brycewang-aer-skills/examples/qte-demo/qte_demo.py	23	the median effect is null, and that the estimated tails match the analytic	STRING
HIGH	…xamples/multiple-testing-demo/multiple_testing_demo.py	16	1. SIZE. With every outcome a true null, the naive "any outcome significant"	STRING
HIGH	…xamples/multiple-testing-demo/multiple_testing_demo.py	19	2. POWER. With one outcome carrying a real effect and the rest null, the	STRING
HIGH	…ls/50-brycewang-aer-skills/templates/python/run_all.py	12	1. Create a virtual env: python -m venv .venv && source .venv/bin/activate	STRING
HIGH	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1017	len(undefined) <= 3, # Allow some tolerance	CODE

AI Slop Vocabulary30 hits · 74 pts

Severity	File	Line	Snippet	Context
MEDIUM	pyproject.toml	4	# script. It does NOT package the skills catalog, the eval harness, or the	COMMENT
MEDIUM	demo-notebooks/statsPAI_pipeline_5.2.py	88	"""Extract robust SE from model t(\|HC\|) or variance-covariance matrix."""	STRING
MEDIUM	…o-notebooks/_r_pipeline_outputs_5.2/lalonde_analysis.R	325	# 6a. Cluster-robust SE (using bootstrapped / clubSandwich for matching)	COMMENT
MEDIUM	eval-harness/run_evals.py	55	# Discrimination fixtures: eval-harness/fixtures/<scenario-id>/{pass,fail}.md.	COMMENT
MEDIUM	tests/test_readme_stats.py	76	# benchmark, eval-harness, and fixtures rows all missing.	COMMENT
MEDIUM	tests/test_readme_stats.py	301	# `eval-harness/fixtures/` must not be read as the `eval-harness/` row,	COMMENT
MEDIUM	scripts/build-catalog-enrich.py	349	# Behavioural depth: which eval-harness scenarios target this skill.	COMMENT
MEDIUM	…w-toolkit/paper-submission/scripts/extract_journals.py	136	"""More robust extraction using the full text line patterns."""	STRING
MEDIUM	…ls/73-brycewang-p-hacking-skills/scripts/phack/grid.py	58	"rdd_inference": ["conventional"], # conventional \| bias_corrected \| robust	CODE
MEDIUM	…3-brycewang-p-hacking-skills/scripts/phack/polyglot.py	1302	# StatsPAI reports the conventional and the robust bias-corrected rows in	COMMENT
MEDIUM⚡	…ls/73-brycewang-p-hacking-skills/scripts/phack/core.py	207	# OLS / WLS with robust / clustered variance	COMMENT
MEDIUM	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	207	# the Wald t rejects but the weak-IV-robust AR test does not: the	COMMENT
MEDIUM	…scholar/skills/hook-development/scripts/hook-linter.sh	3	# Checks hook scripts for common issues and best practices	COMMENT
MEDIUM⚡	…ills/50-brycewang-aer-skills/tests/test_skill_audit.py	101	body = "## Anti-Patterns\n- delve into the literature without naming papers\n"	CODE
MEDIUM	…ewang-aer-skills/examples/dml-plr-demo/dml_plr_demo.py	118	"""Bivariate OLS slope of y on d (with intercept) and its robust (HC0) SE."""	STRING
MEDIUM	…ills/examples/staggered-did-demo/staggered_did_demo.py	93	"""TWFE (biased) and did2s (heterogeneity-robust) aggregate ATTs."""	STRING
MEDIUM	…ization-inference-demo/randomization_inference_demo.py	54	N_TREAT = 5 # unbalanced arm: only 5 treated (leverage 1/5 each)	CODE
MEDIUM	…ization-inference-demo/randomization_inference_demo.py	69	"""HC1 robust t-statistics for OLS of y on [1, D], vectorized over rows	STRING
MEDIUM	…ls/examples/sensitivity-rv-demo/sensitivity_rv_demo.py	167	# robust one.	COMMENT
MEDIUM	…skills/examples/few-clusters-demo/few_clusters_demo.py	2	"""Few-clusters demo: why cluster-robust t-tests need the wild bootstrap.	STRING
MEDIUM	…skills/examples/few-clusters-demo/few_clusters_demo.py	71	"""Slope and cluster-robust t-stat for y on [1, D] (H0: slope = 0)."""	STRING
MEDIUM	…r-skills/examples/shift-share-demo/shift_share_demo.py	85	"""Conventional region-level HC1-robust t-statistic for H0: beta = 0."""	STRING
MEDIUM	skills/50-brycewang-aer-skills/scripts/skill_audit.py	113	# "leverage" as a verb-for-"use"; excludes the econometric noun (leverage	COMMENT
MEDIUM	skills/50-brycewang-aer-skills/scripts/skill_audit.py	114	# diagnostics, high-leverage points).	COMMENT
MEDIUM	skills/50-brycewang-aer-skills/scripts/skill_audit.py	571	negated_section = "## Anti-Patterns\n- delve into the literature without naming papers\n"	CODE
MEDIUM⚡	…s/50-brycewang-aer-skills/templates/python/main_did.py	62	est_method = "dr", # doubly-robust	CODE
MEDIUM⚡	…ills/50-brycewang-aer-skills/templates/r/03_main_did.R	41	est_method = "dr", # doubly-robust	CODE
MEDIUM⚡	…ills/50-brycewang-aer-skills/templates/r/03_main_did.R	85	# period before computing relative-magnitudes robust CIs.	COMMENT
MEDIUM	…riting-skills/skills/typst-paper/scripts/deai_check.py	131	# 3. "comprehensive" followed by range	COMMENT
MEDIUM	…ing-skills/skills/latex-paper-en/scripts/deai_check.py	109	# 3. "comprehensive" followed by range	COMMENT

Synthetic Comment Markers11 hits · 60 pts

Severity	File	Line	Snippet	Context
HIGH	catalog/skills.json	17692	"description": "Run declarative data quality checks and generate a codebook. Checks completeness, distributions, i	CODE
HIGH⚡	docs/SKILL_CATALOG.md	71	\| 48 \| [`44-matsuikentaro1-humanizer_academic`](../skills/44-matsuikentaro1-humanizer_academic/) \| 1 \| MIT \| [source](ht	CODE
HIGH⚡	docs/SKILL_CATALOG.md	75	\| 52 \| [`48-de-AIGC-skills`](../skills/48-de-AIGC-skills/) \| 1 \| CC-BY-SA-4.0 (repository default) \| [source](https://gi	CODE
HIGH⚡	docs/SKILL_CATALOG.md	76	\| 53 \| [`49-voidborne-d-humanize-chinese`](../skills/49-voidborne-d-humanize-chinese/) \| 1 \| MIT Non-Commercial \| [sourc	CODE
HIGH	…kills/obsidian-project-memory/scripts/project_views.py	74	return f'''# Generated by Claude Scholar project_views.py	CODE
HIGH	…ademic-pipeline/agents/integrity_verification_agent.md	59	- Walters, W. H., & Wilder, E. I. (2023). Fabrication and errors in the bibliographic citations generated by ChatGPT. *S	CODE
HIGH	skills/44-matsuikentaro1-humanizer_academic/SKILL.md	772	This skill is based on [Wikipedia:Signs of AI writing](https://en.wikipedia.org/wiki/Wikipedia:Signs_of_AI_writing), mai	CODE
HIGH	…motions-research-methods/skills/data-validate/SKILL.md	6	check results. Produces a pointblank/pandera validation report and an auto-generated codebook.	CODE
HIGH	skills/47-conorbronsdon-avoid-ai-writing/SKILL.md	329	Structure is the #1 detection signal. AI detection tools (including Pangram, which trains a classifier on 28M human	CODE
HIGH	…Research-AI-Research-SKILLs/academic-plotting/SKILL.md	496	├── fig_<name>.png # Raster output (300 DPI, for AI-generated or fallback)	STRING
HIGH	…earch-SKILLs/ml-paper-writing/references/checklists.md	331	- [ ] Work NOT wholly or largely generated by AI (AI editing tools are acceptable)	CODE

Verbosity Indicators25 hits · 51 pts

Severity	File	Line	Snippet	Context
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	20	# Step 1: Navigate to form	COMMENT
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	24	# Step 2: Snapshot to discover form elements	COMMENT
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	29	# Step 3: Fill form fields (customize these refs based on snapshot output)	COMMENT
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	46	# Step 4: Wait for submission	COMMENT
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	50	# Step 5: Verify result	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1487	# Step 1: Extract text	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1495	# Step 2: Detect language	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1504	# Step 3: Determine checks	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1509	# Step 4: Build task list (filter inapplicable checks first)	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1623	# Step 6: Build result	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1985	# Step 2: Parse previous report and any structured issue bundle alongside it.	COMMENT
LOW⚡	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1989	# Step 3: Match and classify each prior issue	COMMENT
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1574	# Step 5: Run checklist (universal + venue-specific)	COMMENT
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1635	# Step 7: ScholarEval (optional)	COMMENT
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1973	# Step 1: Run fresh audit (using quick-audit checks)	COMMENT
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	2039	# Step 4: Identify NEW issues (unmatched in fresh audit)	COMMENT
LOW⚡	…skills/skills/paper-audit/scripts/literature_search.py	586	# Step 1: Extract metadata	COMMENT
LOW⚡	…skills/skills/paper-audit/scripts/literature_search.py	591	# Step 2: Generate queries	COMMENT
LOW⚡	…skills/skills/paper-audit/scripts/literature_search.py	609	# Step 3: Search literature	COMMENT
LOW⚡	…skills/skills/paper-audit/scripts/literature_search.py	616	# Step 4: Filter by relevance	COMMENT
LOW⚡	skills/57-dgunning-edgartools/skills/content/skill.yaml	201	# Step 1: Decide what to demonstrate	COMMENT
LOW⚡	skills/57-dgunning-edgartools/skills/content/skill.yaml	204	# Step 2: Write and test the code	COMMENT
LOW⚡	skills/57-dgunning-edgartools/skills/content/skill.yaml	207	# Step 3: Capture screenshots	COMMENT
LOW⚡	skills/57-dgunning-edgartools/skills/content/skill.yaml	211	# Step 4: Write the article	COMMENT
LOW⚡	skills/57-dgunning-edgartools/skills/content/skill.yaml	215	# Step 5: Verify	COMMENT

Redundant / Tautological Comments27 hits · 42 pts

Severity	File	Line	Snippet	Context
LOW⚡	…nfin-workflow-toolkit/md-to-docx/convert_md_to_docx.py	320	# Check if pandoc is installed	COMMENT
LOW⚡	…nfin-workflow-toolkit/md-to-docx/convert_md_to_docx.py	329	# Check if input file exists	COMMENT
LOW	…lkit/chinese-quote-converter/scripts/convert_quotes.py	73	# Check if it's likely an apostrophe (letter before and after)	COMMENT
LOW	…ence/skills/workflows-work/scripts/worktree-manager.sh	80	# Check if worktree already exists	COMMENT
LOW	…ence/skills/workflows-work/scripts/worktree-manager.sh	186	# Check if we're currently in a worktree	COMMENT
LOW	…e-code-my-workflow/dot-claude/hooks/verify-reminder.py	162	# Check if this file type needs verification	COMMENT
LOW	…/skills/skill-quality-reviewer/scripts/extract-yaml.sh	10	# Check if path provided	COMMENT
LOW	…/skills/skill-quality-reviewer/scripts/extract-yaml.sh	20	# Check if SKILL.md exists	COMMENT
LOW	…scholar/skills/skill-improver/scripts/verify-update.sh	10	# Check if path provided	COMMENT
LOW	…scholar/skills/skill-improver/scripts/verify-update.sh	96	# Check if scripts are executable (macOS compatible)	COMMENT
LOW	…-scholar/skills/skill-improver/scripts/backup-skill.sh	10	# Check if path provided	COMMENT
LOW	…-scholar/skills/skill-improver/scripts/backup-skill.sh	22	# Check if skill path exists	COMMENT
LOW	…holar/skills/hook-development/examples/load-context.sh	17	# Check if TypeScript	COMMENT
LOW	…kills/hook-development/scripts/validate-hook-schema.sh	123	# Check if prompt-based hooks are used on supported events	COMMENT
LOW	…-skills/skills/latex-thesis-zh/scripts/check_tables.py	293	# Check if there are significance markers but no note explaining them	COMMENT
LOW	…skills/skills/latex-thesis-zh/scripts/map_structure.py	108	# Read file content	COMMENT
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	980	# Check if defined as (ACRONYM) or {ACRONYM}	COMMENT
LOW	…kills/skills/paper-audit/scripts/literature_compare.py	128	# Check if this result matches any cited paper	COMMENT
LOW	…c-writing-skills/skills/typst-paper/scripts/compile.py	69	# Check if Typst is installed	COMMENT
LOW	…g-skills/skills/latex-paper-en/scripts/check_tables.py	293	# Check if there are significance markers but no note explaining them	COMMENT
LOW	…hsantanna88-clo-author/dot-claude/hooks/pre-compact.py	210	# Print message	COMMENT
LOW	…Community-daaf/dot-claude/hooks/remind-orchestrator.sh	35	# Check if this is the user's first-ever session	COMMENT
LOW	…ource-countypres/scripts/04_semantic_interpretation.py	57	# Check if "COUNTY" appears in names	COMMENT
LOW	…ource-countypres/scripts/04_semantic_interpretation.py	169	# Check if TOTAL rows still exist for 2020	COMMENT
LOW	…n-data-source-countypres/scripts/03_quality_profile.py	94	# Check if county_fips is unique within state	COMMENT
LOW	…on-data-source-countypres/scripts/05_reconcile_docs.py	146	# Check if modes only appear in 2020	COMMENT
LOW	skills/57-dgunning-edgartools/skills/funds/skill.yaml	44	is_bdc_cik(1287750) # Check if CIK is a BDC → True	CODE

Docstring Block Structure8 hits · 40 pts

Severity	File	Line	Snippet	Context
HIGH	…skills/citation-verification/scripts/format-checker.py	114	加载 BibTeX 文件 Args: file_path: BibTeX 文件路径 Returns: BibTeX 条目列表 Raises: FileNotFou	STRING
HIGH	…skills/citation-verification/scripts/format-checker.py	141	加载 LaTeX 文件 Args: file_path: LaTeX 文件路径 Returns: 文件内容 Raises: FileNotFoundError:	STRING
HIGH	…ar/skills/architecture-design/references/code_style.md	145	Create dataset class by name. Args: data_name: Name of the dataset to create. Returns: Dataset	STRING
HIGH	…ls/kaggle-learner/references/knowledge/.archive/nlp.md	2025	Test-Time Training (TTT) MindsAI 方法：在测试时训练模型 Args: model: 基础模型 train_examples: 训练示例 (input	STRING
HIGH	…gle-learner/references/knowledge/nlp/arc-prize-2025.md	1196	Test-Time Training (TTT) MindsAI 方法：在测试时训练模型 Args: model: 基础模型 train_examples: 训练示例 (input	STRING
HIGH	…c-writing-skills/skills/paper-audit/scripts/parsers.py	69	Extended factory method supporting PDF in addition to LaTeX/Typst. Args: file_path: Path to the docume	STRING
HIGH	skills/57-dgunning-edgartools/skills/__init__.py	39	Get skill by name. Args: name: Skill name (e.g., "EdgarTools") Returns: BaseSkill instanc	STRING
HIGH	skills/57-dgunning-edgartools/skills/base.py	150	Get content of a specific markdown document. Args: name: Document name (with or without .m	STRING

Fake / Example Data34 hits · 40 pts

Severity	File	Line	Snippet	Context
LOW⚡	tests/test_eval_scenarios.py	290	(cand / "statspai-weak-iv.md").write_text("placeholder", encoding="utf-8")	CODE
LOW⚡	tests/test_eval_scenarios.py	291	(cand / "typo-scenario.md").write_text("placeholder", encoding="utf-8")	CODE
LOW⚡	tests/test_eval_scenarios.py	292	(cand / "ignored.csv").write_text("placeholder", encoding="utf-8")	CODE
LOW⚡	tests/test_eval_scenarios.py	322	path.write_text("placeholder", encoding="utf-8")	CODE
LOW⚡	tests/test_eval_scenarios.py	331	bad_candidate.write_text("placeholder", encoding="utf-8")	CODE
LOW⚡	tests/test_de_aigc_provenance_scrub.py	285	self.assertEqual(report["info"]["Author"], "Jane Doe")	CODE
LOW	…lls/67-econfin-workflow-toolkit/agent-browser/SKILL.md	23	agent-browser fill @e1 "user@example.com"	CODE
LOW	…lls/67-econfin-workflow-toolkit/agent-browser/SKILL.md	39	agent-browser fill @e1 "user@example.com" && agent-browser fill @e2 "password123" && agent-browser click @e3	CODE
LOW	…lls/67-econfin-workflow-toolkit/agent-browser/SKILL.md	93	agent-browser fill @e1 "Jane Doe"	CODE
LOW	…low-toolkit/agent-browser/references/authentication.md	31	agent-browser fill @e1 "user@example.com"	CODE
LOW	…low-toolkit/agent-browser/references/authentication.md	50	agent-browser fill @e1 "user@example.com"	CODE
LOW	…low-toolkit/agent-browser/references/authentication.md	107	agent-browser fill @e1 "user@example.com"	CODE
LOW	…flow-toolkit/agent-browser/references/snapshot-refs.md	72	agent-browser fill @e10 "user@example.com"	CODE
LOW	…toolkit/agent-browser/references/session-management.md	29	agent-browser --session auth fill @e1 "user@example.com"	CODE
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	32	# agent-browser fill @e1 "John Doe" # Text input	COMMENT
LOW⚡	…low-toolkit/agent-browser/templates/form-automation.sh	33	# agent-browser fill @e2 "user@example.com" # Email input	COMMENT
LOW	…-workflow-toolkit/stata/references/string-functions.md	9	gen str20 name = "John Doe"	CODE
LOW	…rkflow-toolkit/stata/references/variables-operators.md	29	gen str20 name = "John Doe"	CODE
LOW	…dot-claude/skills/stata/references/string-functions.md	9	gen str20 name = "John Doe"	CODE
LOW	…-claude/skills/stata/references/variables-operators.md	29	gen str20 name = "John Doe"	CODE
LOW⚡	…ar/skills/bug-detective/examples/debugging-workflow.sh	56	# if [ $name = "John Doe" ]; then	COMMENT
LOW⚡	…ar/skills/bug-detective/examples/debugging-workflow.sh	53	local name="John Doe"	CODE
LOW⚡	…ar/skills/bug-detective/examples/debugging-workflow.sh	61	if [ "$name" = "John Doe" ]; then	CODE
LOW	…y-Dawn-claude-scholar/skills/ml-paper-writing/SKILL.md	774	% - Lorem ipsum or placeholder text	CODE
LOW	…ills/webapp-testing/examples/static_html_automation.py	21	page.fill('#name', 'John Doe')	CODE
LOW	…gins/stata/skills/stata/references/string-functions.md	9	gen str20 name = "John Doe"	CODE
LOW	…s/stata/skills/stata/references/variables-operators.md	29	gen str20 name = "John Doe"	CODE
LOW	…lls/latex-to-typst/references/01-document-structure.md	58	("Jane Doe", "John Smith"),	CODE
LOW	…hristopherkenny-skills/skills/latex-to-quarto/SKILL.md	147	author: "Jane Doe"	CODE
LOW	…hristopherkenny-skills/skills/latex-to-quarto/SKILL.md	209	author: "Jane Doe"	CODE
LOW	…/skills/latex-to-quarto/references/01-preamble-yaml.md	42	\| `\author{Jane Doe}` \| `author: "Jane Doe"` \|	CODE
LOW	…72-kaggle-research/kaggle-research/tests/test_smoke.py	20	arguments=("placeholder",),	CODE
LOW	…tion-Community-daaf/dot-claude/agents/data-verifier.md	172	r'coming soon', r'lorem ipsum'	CODE
LOW	…tion-Community-daaf/dot-claude/agents/data-verifier.md	241	# Lorem ipsum and variants	COMMENT

Hallucination Indicators3 hits · 30 pts

Severity	File	Line	Snippet	Context
CRITICAL	…ar/skills/architecture-design/references/code_style.md	46	from src.utils.helpers import import_modules	CODE
CRITICAL	…ar/skills/architecture-design/references/code_style.md	60	from src.utils.helpers import import_modules	CODE
CRITICAL	…r/skills/architecture-design/references/auto_import.md	12	from src.utils.helpers import import_modules	CODE

Self-Referential Comments6 hits · 22 pts

Severity	File	Line	Snippet	Context
MEDIUM	agents/cursor.yaml	14	# This file is not itself a Cursor rule (Cursor expects markdown under	COMMENT
MEDIUM	…ence/skills/workflows-work/scripts/worktree-manager.sh	68	# Create a new worktree	COMMENT
MEDIUM⚡	…hods/skills/research-init/references/templates/setup.R	3	# This file is sourced by _targets.R and provides:	COMMENT
MEDIUM	…ds/skills/research-init/references/templates/targets.R	3	# This file defines the reproducible analysis pipeline using the {targets}	COMMENT
MEDIUM⚡	…ds/skills/research-init/references/templates/targets.R	36	# Define the pipeline	COMMENT
MEDIUM⚡	…de/skills/education-data-query/references/mirrors.yaml	3	# This file is the SINGLE SOURCE OF TRUTH for mirror configuration.	COMMENT

Modern Structural Boilerplate18 hits · 20 pts

Severity	File	Line	Snippet	Context
LOW	aers_score/__init__.py	24	__all__ = ["__version__"]	CODE
LOW	…3-brycewang-p-hacking-skills/scripts/phack/polyglot.py	37	__all__ = ["LANGUAGES", "write_specs", "write_null_columns", "write_runner", "export",	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/race.py	37	__all__ = ["race", "summary_lines", "DEFAULT_PROCEDURES"]	CODE
LOW	…73-brycewang-p-hacking-skills/scripts/phack/theatre.py	27	__all__ = ["build_table", "audit_table"]	CODE
LOW	…3-brycewang-p-hacking-skills/scripts/phack/simulate.py	28	__all__ = ["STRATEGIES", "run_strategy", "false_positive_rate", "sweep",	CODE
LOW⚡	…ls/73-brycewang-p-hacking-skills/scripts/phack/core.py	22	__all__ = [	CODE
LOW	…-brycewang-p-hacking-skills/scripts/phack/inference.py	14	__all__ = ["bonferroni", "sidak", "bh_fdr", "romano_wolf", "min_p_test",	CODE
LOW	…brycewang-p-hacking-skills/scripts/phack/procedures.py	39	__all__ = ["Walk", "Procedure", "Exhaustive", "FirstSignificant", "RandomBudget",	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/detect.py	32	__all__ = ["binomial_test", "fisher_test", "stouffer_test", "lcm_test",	CODE
LOW⚡	…s/73-brycewang-p-hacking-skills/scripts/phack/score.py	18	__all__ = ["CODE_SIGNALS", "scan_code", "score_run", "phi_label"]	CODE
LOW	…r/skills/obsidian-project-memory/scripts/project_kb.py	1695	def update_registry_after_sync(ctx: SyncContext) -> None:	STRING
LOW⚡	…ills/bug-detective/examples/error-handling-patterns.py	11	logger = logging.getLogger(__name__)	CODE
LOW⚡	…ar/skills/bug-detective/examples/debugging-workflow.py	11	logger = logging.getLogger(__name__)	CODE
LOW	…c-writing-skills/skills/paper-audit/scripts/parsers.py	100	__all__ = [	CODE
LOW	…rch/kaggle-research/scripts/kaggle_runtime/__init__.py	13	__all__ = [	CODE
LOW	skills/57-dgunning-edgartools/skills/__init__.py	11	__all__ = [	CODE
LOW	skills/57-dgunning-edgartools/skills/base.py	13	__all__ = ['BaseSkill']	CODE
LOW	skills/57-dgunning-edgartools/skills/core/__init__.py	13	__all__ = ['EdgarToolsSkill', 'edgartools_skill']	CODE

AI Structural Patterns12 hits · 11 pts

Severity	File	Line	Context
LOW	scripts/build-release-notes.py	252	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/grid.py	465	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/race.py	82	CODE
LOW	…3-brycewang-p-hacking-skills/scripts/phack/simulate.py	290	CODE
LOW	…ls/73-brycewang-p-hacking-skills/scripts/phack/core.py	406	CODE
LOW	…-brycewang-p-hacking-skills/scripts/phack/init_card.py	63	CODE
LOW	…/73-brycewang-p-hacking-skills/scripts/phack/search.py	376	CODE
LOW	…brycewang-p-hacking-skills/scripts/phack/procedures.py	300	CODE
LOW	…s/73-brycewang-p-hacking-skills/scripts/phack/score.py	142	CODE
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	804	CODE
LOW	…mic-writing-skills/skills/paper-audit/scripts/audit.py	1418	CODE
LOW	…rch/kaggle-research/scripts/kaggle_runtime/security.py	43	CODE

Example Usage Blocks2 hits · 3 pts

Severity	File	Line	Snippet	Context
LOW	…-literature-workflow/scripts/build_literature_graph.py	248	## How to use	COMMENT
LOW	…kills/architecture-design/examples/pipeline_example.sh	9	# Usage:	COMMENT

Overly Generic Function Names1 hit · 2 pts

Severity	File	Line	Snippet	Context
LOW⚡	…ar/skills/bug-detective/examples/debugging-workflow.py	83	def process_data(data_provider):	CODE

TODO Padding1 hit · 1 pts

Severity	File	Line	Snippet	Context
LOW	…tion-Community-daaf/dot-claude/agents/data-verifier.md	294	\| notebook.py \| 45 \| TODO comment \| `# TODO: implement` \| HIGH \|	CODE

brycewang-stanford/Auto-Empirical-Research-Skills

Maintenance and Governance Review

Risk Review · v3

What These Metrics Mean

Pattern-Signal History

Severity Breakdown

Directory Score Breakdown

Pattern Findings