54yyyu/zotero-mcp

52.3

Adjusted Score

52.3

Raw Score

100%

Time Factor

2026-08-25

Last Push

4.8K

Stars

Python

Language

112.2K

Lines of Code

391

Files

3.7K

Pattern Hits

2026-08-29

Scan Date

0.04

HC Hit Rate

What These Metrics Mean

Adjusted Score: Primary synthetic code indicator. Raw score normalised per 1,000 lines of code and multiplied by the temporal discount factor. This is the definitive comparative metric — use it to rank repositories by AI authorship density.
Raw Score: The unmodified sum of all severity-weighted, context-multiplied pattern match scores before temporal discounting. Reflects the absolute signal strength independent of when the repository was last active.
Time Factor: The temporal discount multiplier (0–100%) applied to the raw score. Repositories last updated before ChatGPT's launch (Nov 2022) receive a 5% factor. Full signal is only assigned to repositories active in the post-adoption era (Jan 2024+).
Pattern Hits: Total count of individual pattern matches across all files and categories. A high hit count with a low score may indicate a very large codebase with isolated AI snippets; a low count with a high score indicates dense, concentrated AI signatures.
HC Hit Rate: High+Critical pattern hits per file, averaged across the repository. This orthogonal signal catches repositories where a few files are densely packed with high-severity AI tells — a strong indicator even when the normalised score appears moderate due to codebase size.
Lines of Code / Files: Total lines and files analysed. The scanner examines 94 file extensions. These denominators are used to normalise the score, enabling fair comparison between repositories of vastly different sizes.

Score History

This chart maps the temporal evolution of the adjusted synthetic code score across successive scan runs. An upward trajectory indicates ongoing incorporation of AI-generated code or expanding LLM-assisted scaffolding; a stable or declining trajectory may reflect active human refactoring, code removal, or the adoption of stricter authorship policies. The dashed secondary line (right axis) independently tracks total raw pattern hit count, which can diverge from the normalised score when codebase size changes significantly between scans.

Severity Breakdown

Classifies detected patterns by their diagnostic confidence and structural impact. CRITICAL patterns (coefficient 10) represent definitive synthetic signatures — hallucinated imports, explicit LLM attribution metadata — virtually never produced by human authors. HIGH (5) indicates strong structural tells such as cross-file repetition or cross-linguistic idioms. MEDIUM (2) covers recognisable conversational padding and AI-specific vocabulary. LOW (1) captures subtle indicators like tautological comments and generic boilerplate that require density to carry independent signal.

CRITICAL 0HIGH 17MEDIUM 859LOW 2863

Directory Score Breakdown

This horizontal bar chart decomposes the repository's raw synthetic code score by top-level directory, allowing you to pinpoint precisely which modules or components carry the highest AI authorship density. Directories with disproportionately high scores relative to their size warrant targeted manual review: concentrated AI signatures often trace back to mass-generated configuration layers, auto-ported test suites, LLM-scaffolded boilerplate classes, or entire subsystems authored under heavy copilot assistance. Use this view to prioritise your human code-review effort.

Pattern Findings

The scanner identified 3739 distinct pattern matches across 20 syntactic categories. Each entry below represents a discrete location in the source code where the engine recorded a statistically significant AI authorship indicator. 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 diagnostic confidence level (CRITICAL / HIGH / MEDIUM / LOW). The Context column identifies whether the match occurred inside executable code, an inline comment, or a string literal — comment-context matches receive a ×1.5 weight because LLMs systematically over-annotate. The ⚡ bolt icon marks clustered matches: three or more patterns within a 10-line window, each receiving an additional ×1.5 density multiplier as dense clusters constitute far stronger evidence of synthetic authorship than isolated hits.

Decorative Section Separators788 hits · 2920 pts

Severity	File	Line	Snippet	Context
MEDIUM⚡	tests/test_page_layout.py	48	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_page_layout.py	50	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_page_layout.py	110	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_page_layout.py	112	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_page_layout.py	212	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_page_layout.py	214	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	23	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	25	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	136	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	138	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	301	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	303	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	560	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_page_layout.py	562	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	37	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	39	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	58	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	60	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	123	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_scite.py	126	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_fulltext_cache.py	186	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_fulltext_cache.py	188	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_citation_import.py	117	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_citation_import.py	119	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	48	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	50	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	160	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	162	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	201	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	203	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	237	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	239	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	677	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	679	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_citation_import.py	420	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	428	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	571	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	573	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	605	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	607	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	330	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	332	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	624	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	626	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_shared_helpers.py	11	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	13	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	57	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	59	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	79	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	81	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	109	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	111	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	138	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	140	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	188	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	190	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	287	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	289	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	313	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	315	# ---------------------------------------------------------------------------	COMMENT
728 more matches not shown…

Hyper-Verbose Identifiers2043 hits · 2036 pts

Severity	File	Line	Snippet	Context
LOW⚡	tests/test_attach_verification.py	79	def test_none_when_attachment_registered(self):	CODE
LOW⚡	tests/test_attach_verification.py	82	def test_none_for_unchanged_entry(self):	CODE
LOW⚡	tests/test_attach_verification.py	86	def test_reports_failure_payload(self):	CODE
LOW⚡	tests/test_attach_verification.py	91	def test_reports_empty_result(self):	CODE
LOW⚡	tests/test_attach_verification.py	95	def test_reports_result_with_no_key(self):	CODE
LOW⚡	tests/test_attach_verification.py	101	def test_rejects_local_client(self):	CODE
LOW	tests/test_attach_verification.py	114	def test_success_passes_through_key(self, dummy_ctx, monkeypatch):	CODE
LOW	tests/test_attach_verification.py	124	def test_failed_upload_falls_back_to_two_step(self, dummy_ctx, monkeypatch):	CODE
LOW	tests/test_attach_verification.py	137	def test_reports_failure_when_two_step_also_fails(self, dummy_ctx, monkeypatch):	CODE
LOW	tests/test_attach_verification.py	153	def test_orphan_shell_deleted_when_upload_fails(self, dummy_ctx, monkeypatch):	CODE
LOW	tests/test_attach_verification.py	167	def test_local_client_fails_fast(self, dummy_ctx):	CODE
LOW	tests/test_set_item_parent.py	18	def test_schema_requires_an_explicit_nullable_parent_key():	CODE
LOW	tests/test_set_item_parent.py	72	def test_sends_minimal_versioned_parent_update(	CODE
LOW	tests/test_set_item_parent.py	94	def test_surfaces_api_exception(monkeypatch):	CODE
LOW	tests/test_set_item_parent.py	105	def test_reports_unsuccessful_response(monkeypatch):	CODE
LOW	tests/test_set_item_parent.py	114	def test_surfaces_item_fetch_error_without_writing(monkeypatch):	CODE
LOW⚡	tests/test_page_layout.py	53	def test_figure_caption_with_colon(self):	CODE
LOW⚡	tests/test_page_layout.py	60	def test_figure_caption_with_period(self):	CODE
LOW⚡	tests/test_page_layout.py	66	def test_fig_abbreviation_with_panel_letter(self):	CODE
LOW⚡	tests/test_page_layout.py	78	def test_supplementary_table_caption(self):	CODE
LOW⚡	tests/test_page_layout.py	84	def test_extended_data_figure_caption(self):	CODE
LOW⚡	tests/test_page_layout.py	90	def test_in_text_reference_rejected(self):	CODE
LOW⚡	tests/test_page_layout.py	94	def test_sentence_starting_with_figure_rejected(self):	CODE
LOW⚡	tests/test_page_layout.py	104	def test_caption_is_case_insensitive(self):	CODE
LOW⚡	tests/test_page_layout.py	180	def test_merges_vertically_adjacent_fragments(self):	CODE
LOW⚡	tests/test_page_layout.py	189	def test_keeps_distant_regions_separate(self):	CODE
LOW⚡	tests/test_page_layout.py	197	def test_dedupes_same_area_keeping_table(self):	CODE
LOW⚡	tests/test_page_layout.py	221	def test_figure_caption_below_figure(self):	CODE
LOW⚡	tests/test_page_layout.py	231	def test_table_caption_above_table(self):	CODE
LOW⚡	tests/test_page_layout.py	240	def test_caption_too_far_not_attached(self):	CODE
LOW⚡	tests/test_page_layout.py	250	def test_two_column_caption_not_cross_attached(self):	CODE
LOW⚡	tests/test_page_layout.py	260	def test_caption_attaches_to_nearest_of_two_stacked_figures(self):	CODE
LOW⚡	tests/test_page_layout.py	708	def test_rejects_invalid_page_number(self, monkeypatch, fake_zot):	CODE
LOW⚡	tests/test_page_layout.py	718	def test_requires_a_zotero_client(self, monkeypatch):	CODE
LOW⚡	tests/test_page_layout.py	728	def test_works_with_local_client_only(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	155	def test_drops_full_page_background(self):	CODE
LOW	tests/test_page_layout.py	164	def test_merges_overlapping_fragments(self):	CODE
LOW	tests/test_page_layout.py	274	def test_each_caption_attaches_to_one_region_only(self):	CODE
LOW	tests/test_page_layout.py	287	def test_region_without_caption_gets_low_confidence(self):	CODE
LOW	tests/test_page_layout.py	317	def test_detects_raster_image_with_caption(self):	CODE
LOW	tests/test_page_layout.py	348	def test_detects_vector_drawing(self):	CODE
LOW	tests/test_page_layout.py	370	def test_detects_table_keeping_table_source(self):	CODE
LOW	tests/test_page_layout.py	400	def test_text_only_page_returns_no_regions(self):	CODE
LOW	tests/test_page_layout.py	418	def test_page_out_of_range_returns_error(self):	CODE
LOW	tests/test_page_layout.py	431	def test_full_page_scan_returns_warning(self):	CODE
LOW	tests/test_page_layout.py	451	def test_missing_cluster_drawings_adds_warning(self, monkeypatch):	CODE
LOW	tests/test_page_layout.py	471	def test_regions_have_sequential_ids_and_normalized_bboxes(self):	CODE
LOW	tests/test_page_layout.py	496	def test_rotated_page_bboxes_stay_normalized(self):	CODE
LOW	tests/test_page_layout.py	518	def test_cropped_page_bboxes_stay_normalized(self):	CODE
LOW	tests/test_page_layout.py	549	def test_invalid_pdf_returns_error(self):	CODE
LOW	tests/test_page_layout.py	611	def test_happy_path_renders_regions_table(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	650	def test_no_regions_returns_guidance(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	661	def test_warnings_are_included(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	675	def test_detection_error_is_returned(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	686	def test_rejects_non_pdf_attachment(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	697	def test_rejects_non_attachment_item(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_gemini_batch.py	38	def test_split_embedding_records_respects_request_limit():	CODE
LOW	tests/test_gemini_batch.py	48	def test_parse_embedding_output_matches_by_key():	CODE
LOW	tests/test_gemini_batch.py	59	def test_parse_embedding_output_falls_back_to_positional_order():	CODE
LOW	tests/test_gemini_batch.py	70	def test_submit_embedding_batches_writes_manifest_and_jsonl(tmp_path):	CODE
1983 more matches not shown…

Excessive Try-Catch Wrapping451 hits · 414 pts

Severity	File	Line	Snippet	Context
LOW	experiments/library-graph-validation/01_build_corpus.py	114	except Exception as e:	STRING
MEDIUM	experiments/library-graph-validation/01_build_corpus.py	111	def main():	CODE
LOW	tests/test_stringified_params.py	44	except Exception:	CODE
LOW⚡	tests/test_stringified_params.py	117	except Exception as exc:	CODE
LOW⚡	tests/test_stringified_params.py	132	except Exception as exc:	CODE
LOW	tests/test_issue_431_server_wedge.py	302	except Exception as exc: # pragma: no cover - failure detail	CODE
MEDIUM	tests/test_issue_431_server_wedge.py	296	def worker(delay):	CODE
LOW⚡	tests/test_ollama_embedding.py	72	except Exception:	CODE
LOW	tests/test_embedding_function_registration.py	132	except Exception:	CODE
LOW	tests/test_description_tokens.py	103	except Exception:	CODE
MEDIUM	tests/test_rate_limiter.py	341	def worker():	CODE
LOW	tests/test_rate_limiter.py	349	except Exception as exc: # pragma: no cover - failure path	CODE
LOW	tests/live/conftest.py	96	except Exception:	CODE
LOW	tests/live/conftest.py	163	except Exception as exc:	CODE
LOW	tests/live/conftest.py	168	except Exception as exc:	CODE
LOW	tests/live/conftest.py	242	except Exception:	CODE
LOW	tests/live/generate_sentinels.py	63	except Exception:	CODE
LOW	tests/live/generate_sentinels.py	106	except Exception as exc:	CODE
LOW	tests/live/_discovery.py	39	except Exception:	CODE
LOW	tests/live/_discovery.py	107	except Exception:	CODE
LOW	scripts/check_openai_ratelimits.py	46	except Exception as e:	CODE
LOW	scripts/check_openai_ratelimits.py	132	except Exception as e:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	123	except Exception:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	147	except Exception as e:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	191	except Exception as e:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	245	except Exception as e:	CODE
MEDIUM	src/zotero_mcp/better_bibtex_client.py	246	print(f"Error searching for cite keys: {e}")	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	319	except Exception as e:	CODE
LOW⚡	src/zotero_mcp/better_bibtex_client.py	401	except Exception as e:	CODE
MEDIUM⚡	src/zotero_mcp/better_bibtex_client.py	402	print(f"Error processing annotation: {e}")	CODE
LOW	src/zotero_mcp/pdf_utils.py	829	except Exception:	CODE
LOW	src/zotero_mcp/config_light.py	52	except Exception as e:	CODE
LOW	src/zotero_mcp/config_light.py	110	except Exception as e:	CODE
LOW	src/zotero_mcp/config_light.py	137	except Exception:	CODE
LOW	src/zotero_mcp/html_metadata.py	164	except Exception:	CODE
LOW	src/zotero_mcp/client.py	264	except Exception:	CODE
LOW	src/zotero_mcp/client.py	399	except Exception:	CODE
LOW	src/zotero_mcp/client.py	506	except Exception as e:	CODE
LOW	src/zotero_mcp/client.py	626	except Exception:	CODE
LOW	src/zotero_mcp/client.py	711	except Exception:	CODE
LOW	src/zotero_mcp/client.py	793	except Exception as exc:	CODE
LOW	src/zotero_mcp/client.py	812	except Exception as exc:	CODE
LOW	src/zotero_mcp/client.py	843	except Exception as exc:	CODE
MEDIUM⚡	src/zotero_mcp/setup_helper.py	557	print(f"Error saving semantic search config: {e}")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	94	print(f"Error searching for zotero-mcp: {e}")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	601	print(f"Error: Config file at {config_path} is not valid JSON. Creating new config.")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	665	print(f"Error writing config file: {str(e)}")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	773	print("Error: Could not find zotero-mcp executable.")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	786	print("Error: Could not determine Claude Desktop config path.")	CODE
LOW⚡	src/zotero_mcp/setup_helper.py	556	except Exception as e:	CODE
LOW⚡	src/zotero_mcp/setup_helper.py	567	except Exception:	CODE
LOW	src/zotero_mcp/setup_helper.py	93	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	583	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	664	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	683	except Exception:	CODE
LOW	src/zotero_mcp/setup_helper.py	867	except Exception:	CODE
LOW	src/zotero_mcp/setup_helper.py	934	except Exception as e:	CODE
LOW	src/zotero_mcp/pdfannots_downloader.py	183	except Exception as e:	CODE
MEDIUM	src/zotero_mcp/pdfannots_downloader.py	184	print(f"Error downloading pdfannots2json: {e}")	CODE
MEDIUM⚡	src/zotero_mcp/cli_standalone.py	936	print(f"Error: {message}", file=sys.stderr)	CODE
391 more matches not shown…

Unused Imports198 hits · 144 pts

Severity	File	Line	Context
LOW	tests/test_set_item_parent.py	3	CODE
LOW	tests/test_shared_helpers.py	4	CODE
LOW	tests/test_shared_helpers.py	4	CODE
LOW	tests/test_toolsets.py	13	CODE
LOW	tests/test_add_by_url.py	7	CODE
LOW	tests/test_include_subcollections.py	18	CODE
LOW	tests/test_delete_item.py	9	CODE
LOW	tests/test_add_by_isbn.py	8	CODE
LOW	tests/test_add_by_isbn.py	10	CODE
LOW	tests/test_stringified_params.py	31	CODE
LOW	tests/test_batch_adapter_compat.py	20	CODE
LOW	tests/test_add_from_file.py	5	CODE
LOW	tests/test_add_from_file.py	6	CODE
LOW	tests/test_add_from_file.py	6	CODE
LOW	tests/test_add_from_file.py	9	CODE
LOW	tests/test_add_from_file.py	9	CODE
LOW	tests/test_update_item.py	3	CODE
LOW	tests/test_token_optimization.py	4	CODE
LOW	tests/test_token_optimization.py	6	CODE
LOW	tests/test_v021_fixes.py	8	CODE
LOW	tests/test_v021_fixes.py	10	CODE
LOW	tests/test_tag_filter_normalization.py	10	CODE
LOW	tests/test_add_by_doi.py	4	CODE
LOW	tests/test_api_lock_bounded.py	14	CODE
LOW	tests/test_search_improvements.py	3	CODE
LOW	tests/test_search_improvements.py	4	CODE
LOW	tests/test_search_improvements.py	5	CODE
LOW	tests/test_zotero_ft_cache.py	22	CODE
LOW	tests/test_pdf_cascade.py	4	CODE
LOW	tests/test_pdf_cascade.py	6	CODE
LOW	tests/test_pdf_cascade.py	17	CODE
LOW	tests/test_item_related.py	3	CODE
LOW	tests/test_regression_bugs.py	8	CODE
LOW	tests/test_duplicates.py	6	CODE
LOW	tests/test_duplicates.py	8	CODE
LOW	tests/_search_corpus.py	21	CODE
LOW	tests/test_search_parity_offline.py	22	CODE
LOW	tests/test_generic_batch_flags.py	177	CODE
LOW	tests/test_generic_batch_flags.py	178	CODE
LOW	tests/test_pdf_outline.py	3	CODE
LOW	tests/test_pdf_outline.py	5	CODE
LOW	tests/test_pdf_outline.py	5	CODE
LOW	tests/live/generate_sentinels.py	42	CODE
LOW	tests/live/test_embedding_sentinels.py	25	CODE
LOW	tests/live/test_fault_injection.py	19	CODE
LOW	tests/live/test_chroma_roundtrip_live.py	19	CODE
LOW	scripts/measure_context_cost.py	25	CODE
LOW	scripts/measure_context_cost.py	100	CODE
LOW	scripts/gen_basefield_map.py	21	CODE
LOW	src/zotero_mcp/webdav.py	3	CODE
LOW	src/zotero_mcp/server.py	14	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
LOW	src/zotero_mcp/server.py	18	CODE
138 more matches not shown…

Deep Nesting118 hits · 71 pts

Severity	File	Line	Context
LOW	…eriments/library-graph-validation/04_build_subgraph.py	47	CODE
LOW	tests/test_chroma_client_real.py	363	CODE
LOW	tests/test_rate_limiter.py	326	CODE
LOW	tests/test_rate_limiter.py	341	CODE
LOW	tests/live/_discovery.py	31	CODE
LOW	scripts/gen_skill_reference.py	60	CODE
LOW	src/zotero_mcp/webdav.py	222	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	126	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	249	CODE
LOW	src/zotero_mcp/config_light.py	57	CODE
LOW	src/zotero_mcp/client.py	461	CODE
LOW	src/zotero_mcp/toolsets.py	148	CODE
LOW	src/zotero_mcp/setup_helper.py	110	CODE
LOW	src/zotero_mcp/setup_helper.py	207	CODE
LOW	src/zotero_mcp/setup_helper.py	521	CODE
LOW	src/zotero_mcp/setup_helper.py	588	CODE
LOW	src/zotero_mcp/setup_helper.py	714	CODE
LOW	src/zotero_mcp/pdfannots_downloader.py	133	CODE
LOW	src/zotero_mcp/cli_standalone.py	193	CODE
LOW	src/zotero_mcp/cli_standalone.py	250	CODE
LOW	src/zotero_mcp/cli_standalone.py	363	CODE
LOW	src/zotero_mcp/cli_standalone.py	413	CODE
LOW	src/zotero_mcp/cli_standalone.py	473	CODE
LOW	src/zotero_mcp/cli_standalone.py	636	CODE
LOW	src/zotero_mcp/updater.py	45	CODE
LOW	src/zotero_mcp/updater.py	122	CODE
LOW	src/zotero_mcp/updater.py	319	CODE
LOW	src/zotero_mcp/local_db.py	1754	CODE
LOW	src/zotero_mcp/epub_utils.py	471	CODE
LOW	src/zotero_mcp/epub_utils.py	703	CODE
LOW	src/zotero_mcp/cli.py	54	CODE
LOW	src/zotero_mcp/cli.py	105	CODE
LOW	src/zotero_mcp/cli.py	434	CODE
LOW	src/zotero_mcp/utils.py	79	CODE
LOW	src/zotero_mcp/utils.py	114	CODE
LOW	src/zotero_mcp/chroma_client.py	48	CODE
LOW	src/zotero_mcp/chroma_client.py	265	CODE
LOW	src/zotero_mcp/citation_import.py	192	CODE
LOW	src/zotero_mcp/citation_import.py	219	CODE
LOW	src/zotero_mcp/citation_import.py	378	CODE
LOW	src/zotero_mcp/citation_import.py	583	CODE
LOW	src/zotero_mcp/pdf_layout.py	140	CODE
LOW	src/zotero_mcp/pdf_layout.py	218	CODE
LOW	src/zotero_mcp/pdf_layout.py	314	CODE
LOW	src/zotero_mcp/fulltext_cache.py	218	CODE
LOW	src/zotero_mcp/gemini_batch.py	267	CODE
LOW	src/zotero_mcp/semantic_search.py	331	CODE
LOW	src/zotero_mcp/semantic_search.py	671	CODE
LOW	src/zotero_mcp/semantic_search.py	1015	CODE
LOW	src/zotero_mcp/semantic_search.py	1302	CODE
LOW	src/zotero_mcp/semantic_search.py	1980	CODE
LOW	src/zotero_mcp/semantic_search.py	2155	CODE
LOW	src/zotero_mcp/semantic_search.py	2776	CODE
LOW	src/zotero_mcp/semantic_search.py	2903	CODE
LOW	src/zotero_mcp/semantic_search.py	3115	CODE
LOW	src/zotero_mcp/semantic_search.py	3138	CODE
LOW	src/zotero_mcp/semantic_search.py	3249	CODE
LOW	src/zotero_mcp/semantic_search.py	3521	CODE
LOW	src/zotero_mcp/semantic_search.py	3598	CODE
LOW	src/zotero_mcp/semantic_search.py	2960	CODE
58 more matches not shown…

Modern AI Meta-Vocabulary12 hits · 38 pts

Severity	File	Line	Snippet	Context
MEDIUM	CHANGELOG.md	92	- `update-db` no longer accepts `chunking.enabled` in silence on the OpenAI Batch API path (#416). The batch path bu	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	3	"C": "### AlphaFold Meets Flow Matching for Generating Protein Ensembles [via-traversal]\n- [claim] Score-matching	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	49	"C": "### Protein Conformation Generation via Force-Guided SE(3) Diffusion Models [SEED]\n- [claim] MD simulations	CODE
MEDIUM	tests/test_fulltext_web_mode.py	320	# --------- Integration tests: update_database orchestration ----------	COMMENT
MEDIUM⚡	tests/test_webdav.py	286	# _webdav_first_attach (shell + PUT orchestration)	COMMENT
MEDIUM⚡	tests/test_trashed_collections.py	23	# Test scaffolding	COMMENT
MEDIUM⚡	tests/test_identifier_lock.py	217	# removed (proving nothing) or deadlocked on its own scaffolding. A flaky or	COMMENT
MEDIUM	src/zotero_mcp/setup_helper.py	240	# Choose embedding model	COMMENT
MEDIUM	src/zotero_mcp/chroma_client.py	542	# Pick the embedding model. config.json is the richer, authoritative source	COMMENT
MEDIUM	src/zotero_mcp/semantic_search.py	2861	# Truncate to fit the configured embedding model's token limit	COMMENT
MEDIUM	src/zotero_mcp/tools/search.py	1519	# guard, but neither loads an embedding model or a Zotero client.	COMMENT
MEDIUM	src/zotero_mcp/tools/search.py	1533	# Read status without loading any embedding model (fast, no network).	COMMENT

Cross-File Repetition7 hits · 35 pts

Severity	File	Snippet	Context
HIGH	tests/test_issue_372_pdf_tools.py	create table items ( itemid integer primary key, itemtypeid int, dateadded text, datemodified text, clientdatemodified t	STRING
HIGH	tests/test_fulltext_sync_watermark.py	create table items ( itemid integer primary key, itemtypeid int, dateadded text, datemodified text, clientdatemodified t	STRING
HIGH	tests/test_collection_scope_expansion.py	create table items ( itemid integer primary key, itemtypeid int, dateadded text, datemodified text, clientdatemodified t	STRING
HIGH	tests/test_linked_file_attachment_download.py	create table items ( itemid integer primary key, itemtypeid int, dateadded text, datemodified text, clientdatemodified t	STRING
HIGH	src/zotero_mcp/openai_batch.py	submit ``adapter``'s pending chunks while they fit the enqueued-token budget. returns the number of newly submitted chun	STRING
HIGH	src/zotero_mcp/gemini_batch.py	submit ``adapter``'s pending chunks while they fit the enqueued-token budget. returns the number of newly submitted chun	STRING
HIGH	src/zotero_mcp/batch_common.py	submit ``adapter``'s pending chunks while they fit the enqueued-token budget. returns the number of newly submitted chun	STRING

AI Slop Vocabulary11 hits · 31 pts

Severity	File	Line	Snippet	Context
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	3	"C": "### AlphaFold Meets Flow Matching for Generating Protein Ensembles [via-traversal]\n- [claim] Score-matching	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	49	"C": "### Protein Conformation Generation via Force-Guided SE(3) Diffusion Models [SEED]\n- [claim] MD simulations	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	89	"C": "### Diffusion Schr\u00f6dinger Bridge Matching [SEED]\n- [claim] Unlike DDMs and Flow Matching Models, which	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	133	"C": "### A DNA language model based on multispecies alignment predicts the effects of genome-wide variants [SEED]\	CODE
MEDIUM	…ents/library-graph-validation/data/graph_contexts.json	133	"C": "### A DNA language model based on multispecies alignment predicts the effects of genome-wide variants [SEED]\	CODE
MEDIUM⚡	tests/test_rate_limiter.py	317	"""on_success must be robust to missing, empty, non-numeric, or zero-limit headers."""	STRING
MEDIUM	src/zotero_mcp/skill_install.py	243	# The command reference does NOT go in the rules directory. A harness that	COMMENT
MEDIUM⚡	src/zotero_mcp/skill_install.py	293	#: Every supported harness: how to detect it, and how to install into it.	COMMENT
MEDIUM⚡	src/zotero_mcp/skill_install.py	295	#: `detect` answers "is this harness in use here?" from what is on disk. It is	COMMENT
MEDIUM⚡	src/zotero_mcp/skill_install.py	296	#: deliberately generous — a directory or file the harness owns is enough,	COMMENT
MEDIUM	src/zotero_mcp/tools/write.py	2193	# changes. The robust fix is the same one noted in add_by_doi's	COMMENT

Cross-Language Confusion5 hits · 28 pts

Severity	File	Line	Snippet	Context
HIGH⚡	tests/test_sql_search_backend.py	218	result = reader.search_items_sql("quantum", item_type="book \|\| journalArticle", group_id=0)	CODE
HIGH	tests/test_better_bibtex_client.py	150	"""BBT answers ``{"KEY": null}`` — a successful RPC carrying no key —	STRING
HIGH	tests/test_bibtex_never_empty.py	9	``{"KGBSSZ3W": null}`` — a successful RPC carrying no key. ``export_bibtex``	STRING
HIGH⚡	tests/test_global_search.py	242	pipes = reader.search_items_sql("Paper", tag=["methods \|\| methodology"], limit=50)	CODE
HIGH	src/zotero_mcp/tools/_helpers.py	457	# A bare JSON scalar (int/float/bool/null) — e.g. an all-digit	COMMENT

Self-Referential Comments9 hits · 27 pts

Severity	File	Line	Snippet	Context
MEDIUM	tests/test_regression_bugs.py	192	# Create a dummy file	COMMENT
MEDIUM	src/zotero_mcp/client.py	251	# Create a local client - library_id 0 is the default for local.	COMMENT
MEDIUM	src/zotero_mcp/pdfannots_downloader.py	155	# Create a temporary directory for the download	COMMENT
MEDIUM	src/zotero_mcp/_app.py	113	# Create an MCP server (fastmcp 2.14+ no longer accepts `dependencies`)	COMMENT
MEDIUM	src/zotero_mcp/tools/write.py	4348	# Create the metadata item. With if_exists='file' and a known DOI,	COMMENT
MEDIUM	src/zotero_mcp/tools/write.py	4362	# Create a basic item	COMMENT
MEDIUM	src/zotero_mcp/tools/retrieval.py	389	# Create a mapping of collection IDs to their data	COMMENT
MEDIUM	src/zotero_mcp/tools/retrieval.py	392	# Create a mapping of parent to child collections	COMMENT
MEDIUM	src/zotero_mcp/tools/annotations.py	1732	# Create the annotation using web client	COMMENT

Modern Structural Boilerplate21 hits · 22 pts

Severity	File	Line	Snippet	Context
LOW⚡	src/zotero_mcp/config.py	21	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/config_light.py	29	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/identifiers.py	24	__all__ = ["normalize_doi"]	CODE
LOW	src/zotero_mcp/client.py	39	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/client.py	134	def set_active_library(library_id: str, library_type: str) -> None:	CODE
LOW	src/zotero_mcp/__init__.py	14	__all__ = ["__version__", "mcp"]	CODE
LOW	src/zotero_mcp/updater.py	23	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/local_db.py	32	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/chroma_client.py	42	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/chroma_client.py	487	def update_metadatas(self, ids: list[str], metadatas: list[dict[str, Any]]) -> None:	CODE
LOW	src/zotero_mcp/fulltext_cache.py	47	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/gemini_batch.py	46	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/extract.py	27	logger = logging.getLogger(__name__)	CODE
LOW⚡	src/zotero_mcp/scite_client.py	19	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/semantic_search.py	50	logger = logging.getLogger(__name__)	CODE
LOW⚡	src/zotero_mcp/tools/scite.py	28	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/embeddings/__init__.py	22	__all__ = ["BaseEmbeddingFunction"]	CODE
LOW	src/zotero_mcp/embeddings/base.py	54	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/embeddings/providers/__init__.py	32	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/embeddings/providers/__init__.py	34	__all__ = [	CODE
LOW	src/zotero_mcp/embeddings/providers/huggingface.py	11	logger = logging.getLogger(__name__)	CODE

Magic Placeholder Names4 hits · 20 pts

Severity	File	Line	Snippet	Context
HIGH	README.md	335	"ZOTERO_API_KEY": "YOUR_API_KEY",	CODE
HIGH	README.md	349	- Click [here](https://www.zotero.org/settings/security#applications) to generate a Zotero API key and replace `YOUR_	CODE
HIGH	README.md	420	zotero-mcp setup --no-local --api-key YOUR_API_KEY --library-id YOUR_LIBRARY_ID	CODE
HIGH	docs/getting-started.md	45	export ZOTERO_API_KEY=your_api_key	CODE

Over-Commented Block28 hits · 18 pts

Severity	File	Line	Snippet	Context
LOW	pyproject.toml	21	dependencies = [	COMMENT
LOW	tests/test_identifier_lock.py	201	t = threading.Thread(target=holder)	COMMENT
LOW	tests/live/conftest.py	121	# server, or a paid provider API using the machine's production config)	COMMENT
LOW	src/zotero_mcp/client.py	41	# Load environment variables	COMMENT
LOW	src/zotero_mcp/setup_helper.py	481	extraction_config = dict(	COMMENT
LOW	src/zotero_mcp/local_db.py	41	# therefore does not widen what the index sees; it only stops extraction	COMMENT
LOW	src/zotero_mcp/local_db.py	221	#	COMMENT
LOW	src/zotero_mcp/local_db.py	281	# returning it) — so a condition needs a DIFFERENT substring depending on the	COMMENT
LOW	src/zotero_mcp/local_db.py	1301		COMMENT
LOW	src/zotero_mcp/cli.py	1161	# Ensure environment is initialized (Claude config or standalone config)	COMMENT
LOW	src/zotero_mcp/chroma_client.py	541		COMMENT
LOW	src/zotero_mcp/semantic_search.py	201	max_chars = max_tokens * 2	COMMENT
LOW	src/zotero_mcp/semantic_search.py	1361	# is safe to write: it extracts under the indexing page	COMMENT
LOW	src/zotero_mcp/semantic_search.py	2361	# (_prepare_index_records) and has no chunking step, so a config	COMMENT
LOW	src/zotero_mcp/tools/write.py	1581	# held the lock across the ENTIRE recursive multi-DOI loop, one PDF	COMMENT
LOW	src/zotero_mcp/tools/write.py	1681	# holding several of them at once deadlock-free.	COMMENT
LOW	src/zotero_mcp/tools/write.py	1921	create_missing_collections: bool = False,	COMMENT
LOW	src/zotero_mcp/tools/write.py	2281	# arXiv always has a free PDF — try to attach it. Outside the lock: the	COMMENT
LOW	src/zotero_mcp/tools/write.py	3921		COMMENT
LOW	src/zotero_mcp/tools/write.py	3941	# prints — is noise to be discarded (#455).	COMMENT
LOW	src/zotero_mcp/tools/search.py	1001	# SQLite backend evaluates the identical rules — see that module's	COMMENT
LOW	src/zotero_mcp/tools/search.py	1041	"and global search has no fallback — the client-side path "	COMMENT
LOW	src/zotero_mcp/tools/_helpers.py	21	from zotero_mcp import client as _client	COMMENT
LOW	src/zotero_mcp/tools/_helpers.py	841	# failure here degrades to "no match" and the caller creates the item,	COMMENT
LOW	src/zotero_mcp/tools/_helpers.py	921	# fetch now sits between the dedup check and the create, so two callers can	COMMENT
LOW	src/zotero_mcp/embeddings/providers/gemini.py	21	# task instruction in the prompt text itself, which empirically shifts	COMMENT
LOW	src/zotero_mcp/embeddings/providers/gemini.py	41	# prefix tokens are reserved separately (see V2_PREFIX_TOKEN_BUDGET).	COMMENT
LOW	src/zotero_mcp/embeddings/providers/openai.py	21	"""	COMMENT

Redundant / Tautological Comments11 hits · 17 pts

Severity	File	Line	Snippet	Context
LOW	src/zotero_mcp/pdfannots_downloader.py	69	# Check if we have a URL for this platform/architecture	COMMENT
LOW⚡	src/zotero_mcp/updater.py	62	# Check if we're in a uv-managed project	COMMENT
LOW⚡	src/zotero_mcp/updater.py	77	# Check if we're in a uv virtual environment	COMMENT
LOW	src/zotero_mcp/updater.py	101	# Check if pipx is available	COMMENT
LOW	src/zotero_mcp/updater.py	468	# Check if update is needed. Only a strictly newer release counts — a	COMMENT
LOW	src/zotero_mcp/cli.py	711	# Check if installed via uv	COMMENT
LOW	src/zotero_mcp/chroma_client.py	103	# Check if the stored config matches what we want; if not, recreate.	COMMENT
LOW	src/zotero_mcp/tools/write.py	4757	# Check if relation already exists (match both URI prefix variants)	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	257	# Check if Zotero with Better BibTeX is running	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	1299	# Check if creation was successful	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	1735	# Check if creation was successful	COMMENT

Structural Annotation Overuse8 hits · 16 pts

Severity	File	Line	Snippet	Context
LOW⚡	docs/integration-test-plan.md	491	### Step 1: Verify all per-phase cleanups were done	COMMENT
LOW⚡	docs/integration-test-plan.md	499	### Step 2: Identify test-created items	COMMENT
LOW⚡	docs/integration-test-plan.md	505	### Step 3: Tell the user to delete manually	COMMENT
LOW	src/zotero_mcp/better_bibtex_client.py	268	# Step 1: Get citation key from item key. BBT's JSON-RPC expects	COMMENT
LOW	src/zotero_mcp/better_bibtex_client.py	286	# Step 2: Export BibTeX using the citation key.	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	799	# Step 2: Batch-fetch the grandparents (papers)	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	823	# Step 3: Map immediate parent keys to stable paper/attachment context.	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	768	# Step 1: Batch-fetch the immediate parents (attachments)	COMMENT

AI Structural Patterns13 hits · 9 pts

Severity	File	Line	Context
LOW	tests/test_update_item.py	13	CODE
LOW	tests/test_update_item.py	59	CODE
LOW	tests/test_update_item.py	86	CODE
LOW	tests/test_update_item.py	122	CODE
LOW	tests/test_remote_embedding_base.py	142	CODE
LOW	src/zotero_mcp/utils.py	450	CODE
LOW	src/zotero_mcp/semantic_search.py	2155	CODE
LOW	src/zotero_mcp/tools/write.py	831	CODE
LOW	src/zotero_mcp/tools/write.py	3730	CODE
LOW	src/zotero_mcp/embeddings/ratelimit.py	62	CODE
LOW	src/zotero_mcp/embeddings/providers/gemini.py	70	CODE
LOW	src/zotero_mcp/embeddings/providers/openai.py	56	CODE
LOW	src/zotero_mcp/embeddings/providers/ollama.py	43	CODE

Verbosity Indicators5 hits · 9 pts

Severity	File	Line	Snippet	Context
LOW	src/zotero_mcp/better_bibtex_client.py	268	# Step 1: Get citation key from item key. BBT's JSON-RPC expects	COMMENT
LOW	src/zotero_mcp/better_bibtex_client.py	286	# Step 2: Export BibTeX using the citation key.	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	799	# Step 2: Batch-fetch the grandparents (papers)	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	823	# Step 3: Map immediate parent keys to stable paper/attachment context.	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	768	# Step 1: Batch-fetch the immediate parents (attachments)	COMMENT

Fake / Example Data5 hits · 6 pts

Severity	File	Line	Snippet	Context
LOW⚡	tests/test_place_field_reads.py	128	fake_data = {	CODE
LOW	tests/test_place_field_reads.py	143	return {"key": key, "data": fake_data}	CODE
LOW	tests/test_add_by_isbn.py	104	"authors": ["Jane Doe"],	CODE
LOW⚡	tests/test_batch_crossref.py	110	monkeypatch.setenv("ZOTERO_MCP_CONTACT_EMAIL", "me@example.org")	CODE
LOW⚡	tests/test_batch_crossref.py	115	assert calls[0]["params"]["mailto"] == "me@example.org"	CODE

Docstring Block Structure1 hit · 5 pts

Severity	File	Line	Snippet	Context
HIGH	src/zotero_mcp/better_bibtex_client.py	250	Export BibTeX for a specific item using its item key. Args: item_key: Zotero item key to e	STRING

Dead Code1 hit · 2 pts

Severity	File	Line	Snippet	Context
MEDIUM	src/zotero_mcp/local_db.py	1039		CODE

Analysis Overview

What These Metrics Mean

Score History

Severity Breakdown

Directory Score Breakdown

Pattern Findings