54yyyu/zotero-mcp

70.4

Adjusted Score

70.4

Raw Score

100%

Time Factor

2026-07-13

Last Push

4.3K

Stars

Python

Language

46.6K

Lines of Code

125

Files

2.0K

Pattern Hits

2026-07-14

Scan Date

0.03

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 4MEDIUM 544LOW 1468

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 2016 distinct pattern matches across 15 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 Separators494 hits · 1812 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_citation_import.py	85	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_citation_import.py	87	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	16	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	18	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	128	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	130	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	169	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	171	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	205	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_citation_import.py	207	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_citation_import.py	388	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	390	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	422	# ---------------------------------------------------------------------------	STRING
MEDIUM⚡	tests/test_citation_import.py	424	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	298	# ---------------------------------------------------------------------------	STRING
MEDIUM	tests/test_citation_import.py	300	# ---------------------------------------------------------------------------	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	308	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_shared_helpers.py	310	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_shared_helpers.py	248	# ---------------------------------------------------------------------------	COMMENT
MEDIUM	tests/test_shared_helpers.py	250	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	109	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	111	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	268	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	270	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	292	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	294	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	434	# ---------------------------------------------------------------------------	COMMENT
MEDIUM⚡	tests/test_add_by_url.py	436	# ---------------------------------------------------------------------------	COMMENT
434 more matches not shown…

Hyper-Verbose Identifiers847 hits · 817 pts

Severity	File	Line	Snippet	Context
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	706	def test_rejects_invalid_page_number(self, monkeypatch, fake_zot):	CODE
LOW⚡	tests/test_page_layout.py	716	def test_requires_a_zotero_client(self, monkeypatch):	CODE
LOW⚡	tests/test_page_layout.py	726	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	648	def test_no_regions_returns_guidance(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	659	def test_warnings_are_included(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	673	def test_detection_error_is_returned(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	684	def test_rejects_non_pdf_attachment(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_page_layout.py	695	def test_rejects_non_attachment_item(self, monkeypatch, fake_zot):	CODE
LOW	tests/test_identifier_fields_markdown.py	61	def test_isbn_omitted_when_empty(self):	CODE
LOW	tests/test_identifier_fields_markdown.py	66	def test_isbn_omitted_when_missing(self):	CODE
LOW	tests/test_identifier_fields_markdown.py	78	def test_issn_omitted_when_empty(self):	CODE
LOW⚡	tests/test_place_field_reads.py	57	def test_place_rendered_for_book(self):	CODE
LOW⚡	tests/test_place_field_reads.py	63	def test_place_rendered_for_book_section(self):	CODE
LOW⚡	tests/test_place_field_reads.py	68	def test_place_rendered_for_thesis(self):	CODE
LOW⚡	tests/test_place_field_reads.py	73	def test_place_without_publisher(self):	CODE
LOW⚡	tests/test_place_field_reads.py	79	def test_place_omitted_when_empty(self):	CODE
LOW⚡	tests/test_place_field_reads.py	85	def test_place_omitted_when_missing(self):	CODE
LOW⚡	tests/test_place_field_reads.py	102	def test_address_rendered_for_book(self):	CODE
LOW⚡	tests/test_place_field_reads.py	107	def test_address_rendered_for_book_section(self):	CODE
LOW⚡	tests/test_place_field_reads.py	112	def test_address_omitted_when_empty(self):	CODE
LOW⚡	tests/test_place_field_reads.py	117	def test_address_omitted_when_missing(self):	CODE
LOW⚡	tests/test_place_field_reads.py	127	def test_place_in_fetch_metadata(self, monkeypatch):	CODE
LOW⚡	tests/test_scite.py	42	def test_get_papers_batch_posts_bare_doi_array(monkeypatch):	CODE
LOW⚡	tests/test_scite.py	63	def test_enrich_items_matches_lowercased_scite_keys(monkeypatch):	CODE
LOW	tests/test_scite.py	98	def test_check_retractions_flags_uppercase_doi(monkeypatch, dummy_ctx, fake_zot):	CODE
LOW⚡	tests/test_citation_import.py	90	def test_parses_single_article(self):	CODE
LOW⚡	tests/test_citation_import.py	141	def test_multiple_authors_split_on_and(self):	CODE
LOW⚡	tests/test_citation_import.py	147	def test_corporate_author_with_llc(self):	CODE
787 more matches not shown…

Excessive Try-Catch Wrapping363 hits · 345 pts

Severity	File	Line	Snippet	Context
LOW⚡	tests/test_ollama_embedding.py	70	except Exception:	CODE
LOW	tests/test_description_tokens.py	95	except Exception:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	110	except Exception:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	134	except Exception as e:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	178	except Exception as e:	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	232	except Exception as e:	CODE
MEDIUM	src/zotero_mcp/better_bibtex_client.py	233	print(f"Error searching for cite keys: {e}")	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	292	except Exception as e:	CODE
MEDIUM	src/zotero_mcp/better_bibtex_client.py	293	print(f"Error exporting BibTeX: {e}")	CODE
LOW⚡	src/zotero_mcp/better_bibtex_client.py	369	except Exception as e:	CODE
MEDIUM⚡	src/zotero_mcp/better_bibtex_client.py	370	print(f"Error processing annotation: {e}")	CODE
LOW	src/zotero_mcp/pdf_utils.py	829	except Exception:	CODE
LOW	src/zotero_mcp/client.py	215	except Exception:	CODE
LOW	src/zotero_mcp/client.py	386	except Exception:	CODE
LOW	src/zotero_mcp/client.py	534	except Exception:	CODE
LOW	src/zotero_mcp/client.py	580	except Exception as exc:	CODE
LOW	src/zotero_mcp/client.py	607	except Exception as exc:	CODE
LOW	src/zotero_mcp/client.py	631	except Exception as e:	CODE
MEDIUM⚡	src/zotero_mcp/setup_helper.py	436	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	469	print(f"Error: Config file at {config_path} is not valid JSON. Creating new config.")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	533	print(f"Error writing config file: {str(e)}")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	640	print("Error: Could not find zotero-mcp executable.")	CODE
MEDIUM	src/zotero_mcp/setup_helper.py	654	print("Error: Could not determine Claude Desktop config path.")	CODE
LOW⚡	src/zotero_mcp/setup_helper.py	435	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	93	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	451	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	532	except Exception as e:	CODE
LOW	src/zotero_mcp/setup_helper.py	551	except Exception:	CODE
LOW	src/zotero_mcp/setup_helper.py	735	except Exception:	CODE
LOW	src/zotero_mcp/setup_helper.py	781	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	416	print("Error: --openai-batch requires ZOTERO_EMBEDDING_MODEL=openai", file=sys.stderr)	CODE
MEDIUM⚡	src/zotero_mcp/cli_standalone.py	422	print("Error: --fulltext requires local mode (ZOTERO_LOCAL=true).", file=sys.stderr)	CODE
MEDIUM⚡	src/zotero_mcp/cli_standalone.py	432	print(f"Error: {stats['error']}", file=sys.stderr)	CODE
MEDIUM	src/zotero_mcp/cli_standalone.py	102	print(f"Error: invalid JSON in --conditions: {e}", file=sys.stderr)	CODE
MEDIUM	src/zotero_mcp/cli_standalone.py	115	print(f"Error: invalid JSON in --filters: {e}", file=sys.stderr)	CODE
MEDIUM	src/zotero_mcp/cli_standalone.py	208	print("Error: provide note text via --text TEXT or --text - (reads stdin)",	CODE
MEDIUM	src/zotero_mcp/cli_standalone.py	344	print(f"Error: invalid JSON in --creators: {e}", file=sys.stderr)	CODE
MEDIUM	src/zotero_mcp/cli_standalone.py	870	print(f"Error: {e}", file=sys.stderr)	CODE
LOW	src/zotero_mcp/cli_standalone.py	869	except Exception as e:	CODE
LOW	src/zotero_mcp/_app.py	42	except Exception:	CODE
LOW	src/zotero_mcp/_app.py	76	except Exception as e:	CODE
MEDIUM	src/zotero_mcp/_app.py	73	def _background_update():	CODE
LOW⚡	src/zotero_mcp/updater.py	71	except Exception:	CODE
LOW⚡	src/zotero_mcp/updater.py	87	except Exception:	CODE
LOW⚡	src/zotero_mcp/updater.py	207	except Exception as e:	CODE
LOW⚡	src/zotero_mcp/updater.py	217	except Exception as e:	CODE
LOW⚡	src/zotero_mcp/updater.py	227	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	41	except Exception:	CODE
LOW	src/zotero_mcp/updater.py	116	except Exception:	CODE
LOW	src/zotero_mcp/updater.py	141	except Exception:	CODE
LOW	src/zotero_mcp/updater.py	162	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	175	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	256	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	268	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	281	except Exception as e:	CODE
LOW	src/zotero_mcp/updater.py	333	except Exception:	CODE
LOW	src/zotero_mcp/updater.py	363	except Exception as e:	CODE
303 more matches not shown…

Unused Imports150 hits · 103 pts

Severity	File	Line	Context
LOW	tests/test_shared_helpers.py	4	CODE
LOW	tests/test_shared_helpers.py	4	CODE
LOW	tests/test_add_by_url.py	7	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_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	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_webdav.py	3	CODE
LOW	tests/test_item_related.py	3	CODE
LOW	tests/test_cli_standalone.py	3	CODE
LOW	tests/test_regression_bugs.py	8	CODE
LOW	tests/test_duplicates.py	3	CODE
LOW	tests/test_duplicates.py	5	CODE
LOW	tests/test_pdf_outline.py	6	CODE
LOW	tests/test_pdf_outline.py	8	CODE
LOW	tests/test_pdf_outline.py	8	CODE
LOW	src/zotero_mcp/webdav.py	3	CODE
LOW	src/zotero_mcp/server.py	13	CODE
LOW	src/zotero_mcp/server.py	16	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	19	CODE
LOW	src/zotero_mcp/server.py	30	CODE
LOW	src/zotero_mcp/server.py	30	CODE
LOW	src/zotero_mcp/server.py	30	CODE
LOW	src/zotero_mcp/server.py	30	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
LOW	src/zotero_mcp/server.py	38	CODE
90 more matches not shown…

Deep Nesting90 hits · 56 pts

Severity	File	Line	Context
LOW	src/zotero_mcp/webdav.py	222	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	113	CODE
LOW	src/zotero_mcp/better_bibtex_client.py	236	CODE
LOW	src/zotero_mcp/client.py	365	CODE
LOW	src/zotero_mcp/client.py	467	CODE
LOW	src/zotero_mcp/setup_helper.py	146	CODE
LOW	src/zotero_mcp/setup_helper.py	408	CODE
LOW	src/zotero_mcp/setup_helper.py	456	CODE
LOW	src/zotero_mcp/setup_helper.py	582	CODE
LOW	src/zotero_mcp/pdfannots_downloader.py	133	CODE
LOW	src/zotero_mcp/cli_standalone.py	86	CODE
LOW	src/zotero_mcp/cli_standalone.py	130	CODE
LOW	src/zotero_mcp/cli_standalone.py	195	CODE
LOW	src/zotero_mcp/cli_standalone.py	241	CODE
LOW	src/zotero_mcp/cli_standalone.py	397	CODE
LOW	src/zotero_mcp/updater.py	45	CODE
LOW	src/zotero_mcp/updater.py	122	CODE
LOW	src/zotero_mcp/updater.py	288	CODE
LOW	src/zotero_mcp/local_db.py	565	CODE
LOW	src/zotero_mcp/local_db.py	761	CODE
LOW	src/zotero_mcp/epub_utils.py	469	CODE
LOW	src/zotero_mcp/epub_utils.py	701	CODE
LOW	src/zotero_mcp/cli.py	101	CODE
LOW	src/zotero_mcp/cli.py	277	CODE
LOW	src/zotero_mcp/utils.py	22	CODE
LOW	src/zotero_mcp/chroma_client.py	852	CODE
LOW	src/zotero_mcp/chroma_client.py	446	CODE
LOW	src/zotero_mcp/chroma_client.py	537	CODE
LOW	src/zotero_mcp/chroma_client.py	684	CODE
LOW	src/zotero_mcp/citation_import.py	153	CODE
LOW	src/zotero_mcp/citation_import.py	180	CODE
LOW	src/zotero_mcp/citation_import.py	339	CODE
LOW	src/zotero_mcp/citation_import.py	525	CODE
LOW	src/zotero_mcp/pdf_layout.py	138	CODE
LOW	src/zotero_mcp/pdf_layout.py	216	CODE
LOW	src/zotero_mcp/pdf_layout.py	312	CODE
LOW	src/zotero_mcp/semantic_search.py	211	CODE
LOW	src/zotero_mcp/semantic_search.py	256	CODE
LOW	src/zotero_mcp/semantic_search.py	756	CODE
LOW	src/zotero_mcp/semantic_search.py	1380	CODE
LOW	src/zotero_mcp/semantic_search.py	1505	CODE
LOW	src/zotero_mcp/semantic_search.py	1851	CODE
LOW	src/zotero_mcp/semantic_search.py	2153	CODE
LOW	src/zotero_mcp/semantic_search.py	2218	CODE
LOW	src/zotero_mcp/tools/write.py	190	CODE
LOW	src/zotero_mcp/tools/write.py	378	CODE
LOW	src/zotero_mcp/tools/write.py	456	CODE
LOW	src/zotero_mcp/tools/write.py	709	CODE
LOW	src/zotero_mcp/tools/write.py	776	CODE
LOW	src/zotero_mcp/tools/write.py	891	CODE
LOW	src/zotero_mcp/tools/write.py	1198	CODE
LOW	src/zotero_mcp/tools/write.py	1712	CODE
LOW	src/zotero_mcp/tools/write.py	2079	CODE
LOW	src/zotero_mcp/tools/write.py	2209	CODE
LOW	src/zotero_mcp/tools/write.py	2516	CODE
LOW	src/zotero_mcp/tools/write.py	2831	CODE
LOW	src/zotero_mcp/tools/write.py	3098	CODE
LOW	src/zotero_mcp/tools/discovery.py	152	CODE
LOW	src/zotero_mcp/tools/discovery.py	288	CODE
LOW	src/zotero_mcp/tools/retrieval.py	116	CODE
30 more matches not shown…

Self-Referential Comments9 hits · 27 pts

Severity	File	Line	Snippet	Context
MEDIUM	tests/test_regression_bugs.py	193	# Create a dummy file	COMMENT
MEDIUM	src/zotero_mcp/client.py	202	# 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	86	# Create an MCP server (fastmcp 2.14+ no longer accepts `dependencies`)	COMMENT
MEDIUM	src/zotero_mcp/tools/write.py	2590	# Create the metadata item. With if_exists='file' and a known DOI,	COMMENT
MEDIUM	src/zotero_mcp/tools/write.py	2604	# Create a basic item	COMMENT
MEDIUM	src/zotero_mcp/tools/retrieval.py	368	# Create a mapping of collection IDs to their data	COMMENT
MEDIUM	src/zotero_mcp/tools/retrieval.py	371	# Create a mapping of parent to child collections	COMMENT
MEDIUM	src/zotero_mcp/tools/annotations.py	1440	# Create the annotation using web client	COMMENT

Structural Annotation Overuse12 hits · 24 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	251	# Step 1: Get citation key from item key. BBT's JSON-RPC expects	COMMENT
LOW	src/zotero_mcp/better_bibtex_client.py	266	# Step 2: Export BibTeX using the citation key.	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2319	# Step 4: Consolidate collections	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2326	# Step 5: Re-parent children (skip duplicate attachments)	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2364	# Step 6: Trash duplicates (move to Zotero Trash, NOT permanent delete)	COMMENT
LOW	src/zotero_mcp/tools/write.py	2308	# Step 3: Consolidate tags	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	664	# Step 2: Batch-fetch the grandparents (papers)	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	688	# Step 3: Map attachment keys to paper titles	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	633	# Step 1: Batch-fetch the immediate parents (attachments)	COMMENT

Modern AI Meta-Vocabulary7 hits · 22 pts

Severity	File	Line	Snippet	Context
MEDIUM	tests/test_fulltext_web_mode.py	279	# --------- Integration tests: update_database orchestration ----------	COMMENT
MEDIUM⚡	tests/test_trashed_collections.py	23	# Test scaffolding	COMMENT
MEDIUM	src/zotero_mcp/setup_helper.py	172	# Choose embedding model	COMMENT
MEDIUM	src/zotero_mcp/chroma_client.py	878	# Pick the embedding model. config.json is the richer, authoritative source	COMMENT
MEDIUM	src/zotero_mcp/semantic_search.py	1923	# Truncate to fit the configured embedding model's token limit	COMMENT
MEDIUM	src/zotero_mcp/tools/search.py	1058	# guard, but neither loads an embedding model or a Zotero client.	COMMENT
MEDIUM	src/zotero_mcp/tools/search.py	1072	# Read status without loading any embedding model (fast, no network).	COMMENT

Magic Placeholder Names4 hits · 20 pts

Severity	File	Line	Snippet	Context
HIGH	README.md	268	"ZOTERO_API_KEY": "YOUR_API_KEY",	CODE
HIGH	README.md	282	- Click [here](https://www.zotero.org/settings/security#applications) to generate a Zotero API key and replace `YOUR_	CODE
HIGH	README.md	353	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

Redundant / Tautological Comments11 hits · 18 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	437	# Check if update is needed	COMMENT
LOW	src/zotero_mcp/cli.py	430	# Check if installed via uv	COMMENT
LOW	src/zotero_mcp/chroma_client.py	496	# Check if the stored config matches what we want; if not, recreate.	COMMENT
LOW	src/zotero_mcp/tools/write.py	2774	# Check if relation already exists (match both URI prefix variants)	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	167	# Check if Zotero with Better BibTeX is running	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	1045	# Check if creation was successful	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	1443	# Check if creation was successful	COMMENT

Verbosity Indicators9 hits · 17 pts

Severity	File	Line	Snippet	Context
LOW	src/zotero_mcp/better_bibtex_client.py	251	# Step 1: Get citation key from item key. BBT's JSON-RPC expects	COMMENT
LOW	src/zotero_mcp/better_bibtex_client.py	266	# Step 2: Export BibTeX using the citation key.	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2319	# Step 4: Consolidate collections	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2326	# Step 5: Re-parent children (skip duplicate attachments)	COMMENT
LOW⚡	src/zotero_mcp/tools/write.py	2364	# Step 6: Trash duplicates (move to Zotero Trash, NOT permanent delete)	COMMENT
LOW	src/zotero_mcp/tools/write.py	2308	# Step 3: Consolidate tags	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	664	# Step 2: Batch-fetch the grandparents (papers)	COMMENT
LOW⚡	src/zotero_mcp/tools/annotations.py	688	# Step 3: Map attachment keys to paper titles	COMMENT
LOW	src/zotero_mcp/tools/annotations.py	633	# Step 1: Batch-fetch the immediate parents (attachments)	COMMENT

Modern Structural Boilerplate7 hits · 8 pts

Severity	File	Line	Snippet	Context
LOW	src/zotero_mcp/client.py	100	def set_active_library(library_id: str, library_type: str) -> None:	CODE
LOW	src/zotero_mcp/updater.py	23	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/local_db.py	20	logger = logging.getLogger(__name__)	CODE
LOW	src/zotero_mcp/chroma_client.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	35	logger = logging.getLogger(__name__)	CODE
LOW⚡	src/zotero_mcp/tools/scite.py	28	logger = logging.getLogger(__name__)	CODE

Fake / Example Data3 hits · 4 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	105	"authors": ["Jane Doe"],	CODE

AI Structural Patterns6 hits · 4 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	src/zotero_mcp/utils.py	161	CODE
LOW	src/zotero_mcp/tools/write.py	1712	CODE

Over-Commented Block4 hits · 2 pts

Severity	File	Line	Snippet	Context
LOW	src/zotero_mcp/client.py	21	)	COMMENT
LOW	src/zotero_mcp/chroma_client.py	161	persisted collection's config (see OpenAIEmbeddingFunction for details).	COMMENT
LOW	src/zotero_mcp/chroma_client.py	181	V2_PREFIX_TOKEN_BUDGET = 20	COMMENT
LOW	src/zotero_mcp/chroma_client.py	881	# The env var only fills the gap when config.json is absent or left at the	COMMENT

Analysis Overview

What These Metrics Mean

Score History

Severity Breakdown

Directory Score Breakdown

Pattern Findings