Repository Analysis

K-Dense-AI/claude-scientific-writer

A general purpose scientific writer

29.5 Moderate AI signal View on GitHub

Analysis Overview

This report presents the forensic synthetic code analysis of K-Dense-AI/claude-scientific-writer, a Python project with 2,264 GitHub stars. SynthScan v2.0 examined 373,792 lines of code across 1368 source files, recording 4006 pattern matches distributed across 18 syntactic categories. The overall adjusted score of 29.5 places this repository in the Moderate AI signal band.

The scanner applied 160+ deterministic lexical heuristics, multi-line block detectors, abstract syntax tree depth profilers, and a cross-file Jaccard similarity matrix to construct a statistically normalised synthetic code estimate. All matches are individually weighted by severity coefficient and contextual multiplier before summation, and the resulting headline score is temporally discounted to account for the repository's development history relative to the commercial emergence of large language model coding tooling (November 2022 onward).

29.5
Adjusted Score
29.5
Raw Score
100%
Time Factor
2026-08-19
Last Push
2.3K
Stars
Python
Language
373.8K
Lines of Code
1.4K
Files
4.0K
Pattern Hits
2026-08-29
Scan Date
1.18
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 1618MEDIUM 419LOW 1969

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 4006 distinct pattern matches across 18 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.

Cross-File Repetition1479 hits · 7395 pts
SeverityFileLineSnippetContext
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0pure helpers for building manuscript-ready research packets.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0pure helpers for building manuscript-ready research packets.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0pure helpers for building manuscript-ready research packets.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0return a stable url for deduplication without tracking parameters.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0return a stable url for deduplication without tracking parameters.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0return a stable url for deduplication without tracking parameters.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0normalize a title for conservative duplicate detection.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0normalize a title for conservative duplicate detection.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0normalize a title for conservative duplicate detection.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0join source title and excerpts into searchable text.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0join source title and excerpts into searchable text.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0join source title and excerpts into searchable text.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0extract the first doi from text and strip sentence punctuation.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0extract the first doi from text and strip sentence punctuation.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0extract the first doi from text and strip sentence punctuation.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0extract a simple labeled metadata value from source text.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0extract a simple labeled metadata value from source text.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0extract a simple labeled metadata value from source text.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0split excerpts into useful, reasonably bounded sentences.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0split excerpts into useful, reasonably bounded sentences.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0split excerpts into useful, reasonably bounded sentences.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0map external evidence to manuscript sections without using results.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0map external evidence to manuscript sections without using results.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0map external evidence to manuscript sections without using results.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0merge duplicate search/extract records by doi, pmid, url, or title.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0merge duplicate search/extract records by doi, pmid, url, or title.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0merge duplicate search/extract records by doi, pmid, url, or title.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0convert a source into a structured evidence-matrix record.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0convert a source into a structured evidence-matrix record.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0convert a source into a structured evidence-matrix record.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0sort by exclusion status, verification, quality, and recency.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0sort by exclusion status, verification, quality, and recency.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0sort by exclusion status, verification, quality, and recency.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0build a structured packet without adding facts beyond source excerpts.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0build a structured packet without adding facts beyond source excerpts.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0build a structured packet without adding facts beyond source excerpts.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render a conservative citation without inventing missing metadata.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0render a conservative citation without inventing missing metadata.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render a conservative citation without inventing missing metadata.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render the packet as a concise, source-linked markdown artifact.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0render the packet as a concise, source-linked markdown artifact.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render the packet as a concise, source-linked markdown artifact.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render minimal bibtex records using only verified metadata.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0render minimal bibtex records using only verified metadata.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0render minimal bibtex records using only verified metadata.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0write reproducible packet artifacts and return their paths.STRING
HIGHskills/research-lookup/scripts/manuscript_packet.py0write reproducible packet artifacts and return their paths.STRING
HIGH…de/skills/research-lookup/scripts/manuscript_packet.py0write reproducible packet artifacts and return their paths.STRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0parallel-first research retrieval for manuscript evidence compilation. the public ``researchlookup`` class and cli remaiSTRING
HIGHskills/research-lookup/scripts/research_lookup.py0parallel-first research retrieval for manuscript evidence compilation. the public ``researchlookup`` class and cli remaiSTRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0parallel-first research retrieval for manuscript evidence compilation. the public ``researchlookup`` class and cli remaiSTRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0research lookup with parallel search as the stable default backend.STRING
HIGHskills/research-lookup/scripts/research_lookup.py0research lookup with parallel search as the stable default backend.STRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0research lookup with parallel search as the stable default backend.STRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0initialize routing and retrieval options. ``parallel`` remains a compatibility alias for the explicit ``research`` backeSTRING
HIGHskills/research-lookup/scripts/research_lookup.py0initialize routing and retrieval options. ``parallel`` remains a compatibility alias for the explicit ``research`` backeSTRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0initialize routing and retrieval options. ``parallel`` remains a compatibility alias for the explicit ``research`` backeSTRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0select search by default; provider changes require explicit intent.STRING
HIGHskills/research-lookup/scripts/research_lookup.py0select search by default; provider changes require explicit intent.STRING
HIGH…aude/skills/research-lookup/scripts/research_lookup.py0select search by default; provider changes require explicit intent.STRING
1419 more matches not shown…
Excessive Try-Catch Wrapping719 hits · 1053 pts
SeverityFileLineSnippetContext
LOW…aude/skills/research-lookup/scripts/research_lookup.py936 except Exception as exc:CODE
LOW…aude/skills/research-lookup/scripts/research_lookup.py951 except Exception as fallback_exc:CODE
LOW…aude/skills/research-lookup/scripts/research_lookup.py1167 except Exception as exc:STRING
MEDIUM…aude/skills/research-lookup/scripts/research_lookup.py1168 print(f"Error: {exc}", file=sys.stderr)STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py33 print("Error: requests library not found. Install with: pip install requests")CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py307 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py410 except Exception as e:CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py567 except Exception as e:CODE
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py801 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py810 print("Error: Iterations must be between 1 and 2")STRING
LOW…scientific-schematics/scripts/generate_schematic_ai.py830 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py154 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py168 print(f"Error: AI generation script not found: {ai_script}")STRING
LOW…ls/scientific-schematics/scripts/generate_schematic.py189 except Exception as e:STRING
MEDIUM…ls/scientific-schematics/scripts/generate_schematic.py190 print(f"Error executing AI generation: {e}")STRING
MEDIUM…skills/citation-management/scripts/extract_metadata.py134 print(f'Error: CrossRef API returned status {response.status_code} for DOI: {doi}', file=sys.stderr)CODE
LOW…skills/citation-management/scripts/extract_metadata.py137 except Exception as e:CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py138 print(f'Error extracting metadata from DOI {doi}: {e}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py174 print(f'Error: No article found for PMID: {pmid}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py206 print(f'Error: PubMed API returned status {response.status_code} for PMID: {pmid}', file=sys.stderr)CODE
LOW…skills/citation-management/scripts/extract_metadata.py209 except Exception as e:CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py210 print(f'Error extracting metadata from PMID {pmid}: {e}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py239 print(f'Error: No entry found for arXiv ID: {arxiv_id}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py276 print(f'Error: arXiv API returned status {response.status_code} for ID: {arxiv_id}', file=sys.stderr)CODE
LOW…skills/citation-management/scripts/extract_metadata.py279 except Exception as e:CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py280 print(f'Error extracting metadata from arXiv {arxiv_id}: {e}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py480 print(f'Error: Unknown identifier type: {identifier}', file=sys.stderr)CODE
LOW…skills/citation-management/scripts/extract_metadata.py523 except Exception as e:CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py524 print(f'Error reading input file: {e}', file=sys.stderr)CODE
MEDIUM…skills/citation-management/scripts/extract_metadata.py546 print('Error: No successful extractions', file=sys.stderr)CODE
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py33 print("Error: requests library not found. Install with: pip install requests")CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py307 except Exception as e:CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py410 except Exception as e:CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py567 except Exception as e:CODE
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py801 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py810 print("Error: Iterations must be between 1 and 2")STRING
LOW…s/citation-management/scripts/generate_schematic_ai.py830 except Exception as e:STRING
LOW…de/skills/citation-management/scripts/format_bibtex.py40 except Exception as e:CODE
MEDIUM…de/skills/citation-management/scripts/format_bibtex.py41 print(f'Error reading file: {e}', file=sys.stderr)CODE
LOW…de/skills/citation-management/scripts/format_bibtex.py287 except Exception as e:CODE
MEDIUM…de/skills/citation-management/scripts/format_bibtex.py288 print(f'Error writing file: {e}', file=sys.stderr)CODE
MEDIUM…ills/citation-management/scripts/generate_schematic.py154 print("Error: OPENROUTER_API_KEY not found")STRING
MEDIUM…ills/citation-management/scripts/generate_schematic.py168 print(f"Error: AI generation script not found: {ai_script}")STRING
LOW…ills/citation-management/scripts/generate_schematic.py189 except Exception as e:STRING
MEDIUM…ills/citation-management/scripts/generate_schematic.py190 print(f"Error executing AI generation: {e}")STRING
LOW…s/citation-management/scripts/search_google_scholar.py44 except Exception as e:CODE
MEDIUM…s/citation-management/scripts/search_google_scholar.py64 print('Error: scholarly library not installed', file=sys.stderr)CODE
LOW…s/citation-management/scripts/search_google_scholar.py110 except Exception as e:CODE
MEDIUM…s/citation-management/scripts/search_google_scholar.py111 print(f'Error during search: {e}', file=sys.stderr)CODE
LOW…ills/citation-management/scripts/validate_citations.py56 except Exception as e:CODE
MEDIUM…ills/citation-management/scripts/validate_citations.py57 print(f'Error reading file: {e}', file=sys.stderr)CODE
LOW…ills/citation-management/scripts/validate_citations.py236 except Exception:CODE
LOW…ills/citation-management/scripts/validate_citations.py316 except Exception as e:CODE
MEDIUM…ills/citation-management/scripts/validate_citations.py317 print(f'Error reading manuscript file {filepath}: {e}', file=sys.stderr)CODE
MEDIUM…de/skills/citation-management/scripts/doi_to_bibtex.py59 print(f'Error: DOI not found: {doi}', file=sys.stderr)CODE
MEDIUM…de/skills/citation-management/scripts/doi_to_bibtex.py62 print(f'Error: Failed to retrieve BibTeX for {doi} (status {response.status_code})', file=sys.stderr)CODE
MEDIUM…de/skills/citation-management/scripts/doi_to_bibtex.py66 print(f'Error: Request timeout for DOI: {doi}', file=sys.stderr)CODE
MEDIUM…de/skills/citation-management/scripts/doi_to_bibtex.py69 print(f'Error: Request failed for {doi}: {e}', file=sys.stderr)CODE
MEDIUM…de/skills/citation-management/scripts/doi_to_bibtex.py150 print(f'Error: Input file not found: {args.input}', file=sys.stderr)CODE
LOW…de/skills/citation-management/scripts/doi_to_bibtex.py152 except Exception as e:CODE
659 more matches not shown…
Deep Nesting523 hits · 500 pts
SeverityFileLineSnippetContext
LOW…de/skills/research-lookup/scripts/manuscript_packet.py433CODE
LOW…aude/skills/research-lookup/scripts/research_lookup.py603CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py36CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py233CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py340CODE
LOW…scientific-schematics/scripts/generate_schematic_ai.py418CODE
LOW…ls/scientific-schematics/scripts/generate_schematic.py43CODE
LOW…skills/citation-management/scripts/extract_metadata.py141CODE
LOW…skills/citation-management/scripts/extract_metadata.py213CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py36CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py233CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py340CODE
LOW…s/citation-management/scripts/generate_schematic_ai.py418CODE
LOW…de/skills/citation-management/scripts/format_bibtex.py201CODE
LOW…de/skills/citation-management/scripts/format_bibtex.py213CODE
LOW…ills/citation-management/scripts/generate_schematic.py43CODE
LOW…s/citation-management/scripts/search_google_scholar.py47CODE
LOW…ills/citation-management/scripts/validate_citations.py95CODE
LOW…ills/citation-management/scripts/validate_citations.py341CODE
LOW…de/skills/citation-management/scripts/search_pubmed.py98CODE
LOW…de/skills/citation-management/scripts/search_pubmed.py154CODE
LOW.claude/skills/xlsx/scripts/recalc.py81CODE
LOW.claude/skills/xlsx/scripts/recalc.py164CODE
LOW.claude/skills/xlsx/scripts/office/validators/docx.py69CODE
LOW.claude/skills/xlsx/scripts/office/validators/docx.py115CODE
LOW.claude/skills/xlsx/scripts/office/validators/docx.py260CODE
LOW.claude/skills/xlsx/scripts/office/validators/docx.py316CODE
LOW.claude/skills/xlsx/scripts/office/validators/docx.py409CODE
LOW…ude/skills/xlsx/scripts/office/validators/redlining.py181CODE
LOW…ude/skills/xlsx/scripts/office/validators/redlining.py252CODE
LOW.claude/skills/xlsx/scripts/office/validators/pptx.py228CODE
LOW.claude/skills/xlsx/scripts/office/validators/pptx.py270CODE
LOW.claude/skills/xlsx/scripts/office/validators/pptx.py376CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py127CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py218CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py310CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py408CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py494CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py517CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py661CODE
LOW.claude/skills/xlsx/scripts/office/validators/base.py728CODE
LOW.claude/skills/xlsx/scripts/office/helpers/__init__.py85CODE
LOW.claude/skills/pdf/scripts/fill_fillable_fields.py11CODE
LOW.claude/skills/pdf/scripts/fill_fillable_fields.py55CODE
LOW.claude/skills/pdf/scripts/extract_form_field_info.py19CODE
LOW.claude/skills/pdf/scripts/extract_form_field_info.py47CODE
LOW.claude/skills/pdf/scripts/extract_form_structure.py20CODE
LOW.claude/skills/pdf/scripts/check_bounding_boxes.py15CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py39CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py370CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py624CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py807CODE
LOW…de/skills/infographics/scripts/generate_infographic.py56CODE
LOW.claude/skills/pptx-posters/scripts/_manifest.py763CODE
LOW.claude/skills/pptx-posters/scripts/_pptx.py787CODE
LOW.claude/skills/pptx-posters/scripts/_pptx.py1112CODE
LOW.claude/skills/pptx-posters/scripts/_pptx.py1321CODE
LOW.claude/skills/pptx-posters/scripts/_pptx.py1405CODE
LOW.claude/skills/treatment-plans/scripts/_common.py711CODE
LOW.claude/skills/treatment-plans/scripts/_common.py895CODE
463 more matches not shown…
Hyper-Verbose Identifiers466 hits · 486 pts
SeverityFileLineSnippetContext
LOWtests/test_utils.py15 def test_reads_bibliographystyle_from_tex(self, tmp_path):CODE
LOWtests/test_utils.py20 def test_reads_biblatex_style_option(self, tmp_path):CODE
LOWtests/test_utils.py25 def test_defaults_to_bibtex_without_tex(self):CODE
LOWtests/test_utils.py28 def test_defaults_to_bibtex_when_tex_has_no_style(self, tmp_path):CODE
LOWtests/test_utils.py46 def test_topic_match_with_search_keyword(self, tmp_path):CODE
LOWtests/test_utils.py52 def test_new_paper_request_returns_none(self, tmp_path):CODE
LOWtests/test_utils.py57def test_count_citations_in_bib(tmp_path):CODE
LOWtests/test_utils.py64def test_count_citations_ignores_bibtex_directives(tmp_path):CODE
LOWtests/test_utils.py76def test_count_words_preserves_formatted_text_and_ignores_preamble(tmp_path):CODE
LOWtests/test_utils.py90def test_extract_title_handles_nested_braces(tmp_path):CODE
LOWtests/test_utils.py97def test_scan_directory_reports_generic_artifacts_and_sources(tmp_path):CODE
LOWtests/test_agent_plugin.py56def test_shipped_plugin_roots_conform(root):CODE
LOWtests/test_agent_plugin.py60def test_shipped_manifest_version_matches_pyproject():CODE
LOWtests/test_agent_plugin.py66def test_every_repository_skill_is_discoverable():CODE
LOWtests/test_agent_plugin.py82def test_missing_manifest_rejects_the_plugin(tmp_path):CODE
LOWtests/test_agent_plugin.py91def test_unsupported_spec_version_is_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py98def test_invalid_name_is_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py104def test_valid_names_are_accepted(tmp_path):CODE
LOWtests/test_agent_plugin.py110def test_unknown_top_level_field_is_reported_but_not_fatal(tmp_path):CODE
LOWtests/test_agent_plugin.py117def test_non_object_extensions_is_reported_but_not_fatal(tmp_path):CODE
LOWtests/test_agent_plugin.py124def test_extension_namespace_must_be_reverse_domain(tmp_path):CODE
LOWtests/test_agent_plugin.py129def test_reverse_domain_extension_namespace_is_accepted(tmp_path):CODE
LOWtests/test_agent_plugin.py137def test_author_object_rejects_unknown_fields(tmp_path):CODE
LOWtests/test_agent_plugin.py148def test_nested_skills_are_not_discovered(tmp_path):CODE
LOWtests/test_agent_plugin.py158def test_skill_name_must_match_directory(tmp_path):CODE
LOWtests/test_agent_plugin.py163def test_skill_description_length_is_enforced(tmp_path):CODE
LOWtests/test_agent_plugin.py169def test_skill_metadata_mapping_is_parsed(tmp_path):CODE
LOWtests/test_agent_plugin.py181def test_invalid_skill_does_not_invalidate_the_plugin(tmp_path):CODE
LOWtests/test_agent_plugin.py191def test_skills_path_that_is_not_a_directory_invalidates_the_component(tmp_path):CODE
LOWtests/test_agent_plugin.py202def test_valid_mcp_document_passes(tmp_path):CODE
LOWtests/test_agent_plugin.py216def test_mcp_command_escaping_the_plugin_root_is_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py222def test_mcp_relative_command_leaving_root_is_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py228def test_mcp_reserved_env_names_are_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py237def test_mcp_unknown_transport_is_rejected(tmp_path):CODE
LOWtests/test_agent_plugin.py243def test_unexpandable_placeholder_is_warned(tmp_path):CODE
LOWtests/test_agent_plugin.py254def test_mcp_json_that_is_not_a_file_invalidates_the_component(tmp_path):CODE
LOWtests/test_agent_plugin.py265def test_vendored_schemas_declare_their_canonical_ids():CODE
LOWtests/test_agent_plugin.py272def test_non_canonical_schema_id_is_rejected():CODE
LOWtests/test_docs.py21def test_documented_example_files_exist():CODE
LOWtests/test_docs.py26def test_plugin_templates_are_generated_from_canonical_instructions():CODE
LOWtests/test_docs.py34def test_agents_md_mirrors_claude_md():CODE
LOWtests/test_docs.py41def test_instruction_surfaces_do_not_reference_removed_parallel_wrapper():CODE
LOWtests/test_docs.py56def test_skills_document_has_one_section_per_locked_skill():CODE
LOWtests/test_docs.py63def test_first_party_markdown_file_links_resolve():CODE
LOWtests/test_core.py32def test_copies_claude_dir_when_missing(tmp_path):CODE
LOWtests/test_core.py46def test_refreshes_bundled_skills_when_claude_exists(tmp_path):CODE
LOWtests/test_core.py70def test_preserves_user_files_when_refreshing(tmp_path):CODE
LOWtests/test_core.py91def test_agents_dir_receives_the_payload_when_the_project_uses_it(tmp_path):CODE
LOWtests/test_core.py106def test_agents_dir_is_not_created_when_absent(tmp_path):CODE
LOWtests/test_core.py120def test_bundled_payload_can_be_shipped_as_dot_agents(tmp_path):CODE
LOWtests/test_core.py134def test_plugin_manifest_is_refreshed_on_upgrade(tmp_path):CODE
LOWtests/test_core.py148def test_instructions_are_found_across_layouts(tmp_path):CODE
LOWtests/test_core.py169def test_missing_instructions_fall_back_with_a_warning(tmp_path, caplog):CODE
LOWtests/test_core.py180def test_missing_bundle_logs_warning_instead_of_silence(tmp_path, caplog):CODE
LOWtests/test_core.py192def test_stop_hook_blocks_once_then_allows_stop():CODE
LOWtests/test_core.py207def test_stop_hook_disabled_allows_stop():CODE
LOWtests/test_core.py217def test_resolve_auto_continue_environment_override():CODE
LOWtests/test_core.py223def test_relative_output_folder_is_anchored_to_cwd(tmp_path):CODE
LOWtests/test_core.py227def test_create_output_project_is_collision_safe(tmp_path):CODE
LOWtests/test_core.py243def test_explicit_data_files_resolve_against_cwd(tmp_path):CODE
406 more matches not shown…
Magic Placeholder Names94 hits · 365 pts
SeverityFileLineSnippetContext
HIGH…scientific-schematics/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…skills/citation-management/references/pubmed_search.md385 api_key=YOUR_API_KEYCODE
HIGH…skills/citation-management/references/pubmed_search.md418 api_key=YOUR_API_KEYCODE
HIGH…skills/citation-management/references/pubmed_search.md442 api_key=YOUR_API_KEYCODE
HIGH…s/citation-management/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/citation-management/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ills/citation-management/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/citation-management/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…skills/infographics/scripts/generate_infographic_ai.py1308 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…skills/infographics/scripts/generate_infographic_ai.py1309 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…de/skills/infographics/scripts/generate_infographic.py241 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…de/skills/infographics/scripts/generate_infographic.py242 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…skills/literature-review/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…skills/literature-review/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…/skills/latex-posters/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…/skills/latex-posters/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ude/skills/latex-posters/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ude/skills/latex-posters/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py727 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py728 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…skills/scientific-slides/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…skills/scientific-slides/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ills/scientific-slides/scripts/generate_slide_image.py155 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/scientific-slides/scripts/generate_slide_image.py156 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHdocs/API.md366 api_key="sk-ant-your-api-key-here"CODE
HIGH…scientific-schematics/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…scientific-schematics/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ls/scientific-schematics/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/citation-management/references/pubmed_search.md385 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md418 api_key=YOUR_API_KEYCODE
HIGHskills/citation-management/references/pubmed_search.md442 api_key=YOUR_API_KEYCODE
HIGH…s/citation-management/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/citation-management/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…ills/citation-management/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…ills/citation-management/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py1308 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic_ai.py1309 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/infographics/scripts/generate_infographic.py241 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/infographics/scripts/generate_infographic.py242 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/literature-review/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/literature-review/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/literature-review/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/latex-posters/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/latex-posters/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGHskills/latex-posters/scripts/generate_schematic.py159 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py803 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…lls/scientific-slides/scripts/generate_schematic_ai.py804 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py727 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
HIGH…s/scientific-slides/scripts/generate_slide_image_ai.py728 print("\nOr add OPENROUTER_API_KEY=your_api_key to a .env file")STRING
HIGHskills/scientific-slides/scripts/generate_schematic.py158 print(" export OPENROUTER_API_KEY='your_api_key'")STRING
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Unused Imports348 hits · 348 pts
SeverityFileLineSnippetContext
LOWexample_api_usage.py3CODE
LOW…de/skills/research-lookup/scripts/manuscript_packet.py3CODE
LOW…aude/skills/research-lookup/scripts/research_lookup.py9CODE
LOW…de/skills/citation-management/scripts/format_bibtex.py10CODE
LOW…aude/skills/markitdown/scripts/inspect_installation.py4CODE
LOW…aude/skills/markitdown/scripts/inspect_installation.py45CODE
LOW.claude/skills/markitdown/scripts/convert_literature.py4CODE
LOW.claude/skills/markitdown/scripts/batch_convert.py8CODE
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py5CODE
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py6CODE
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py7CODE
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py8CODE
LOW…laude/skills/xlsx/scripts/office/helpers/pptx_chart.py8CODE
LOW…laude/skills/xlsx/scripts/office/helpers/pptx_slide.py8CODE
LOW…laude/skills/xlsx/scripts/office/helpers/pptx_theme.py8CODE
LOW.claude/skills/pptx-posters/scripts/plan_export.py4CODE
LOW.claude/skills/pptx-posters/scripts/_manifest.py4CODE
LOW.claude/skills/pptx-posters/scripts/_pptx.py4CODE
LOW.claude/skills/pptx-posters/scripts/check_layout.py4CODE
LOW.claude/skills/pptx-posters/scripts/inventory_images.py4CODE
LOW.claude/skills/pptx-posters/scripts/_common.py4CODE
LOW…laude/skills/pptx-posters/scripts/validate_manifest.py4CODE
LOW.claude/skills/pptx-posters/scripts/inspect_pptx.py4CODE
LOW.claude/skills/pptx-posters/scripts/check_palette.py4CODE
LOW.claude/skills/pptx-posters/scripts/generate_poster.py4CODE
LOW…e/skills/treatment-plans/scripts/check_completeness.py4CODE
LOW…lls/treatment-plans/scripts/validate_treatment_plan.py4CODE
LOW…kills/treatment-plans/scripts/validate_traceability.py4CODE
LOW.claude/skills/treatment-plans/scripts/_common.py4CODE
LOW…kills/treatment-plans/scripts/privacy_process_check.py4CODE
LOW…de/skills/treatment-plans/scripts/check_consistency.py4CODE
LOW…e/skills/treatment-plans/scripts/timeline_generator.py4CODE
LOW…de/skills/treatment-plans/scripts/generate_template.py4CODE
LOW…ills/scientific-writing/scripts/validate_authorship.py3CODE
LOW…ills/scientific-writing/scripts/scaffold_manuscript.py3CODE
LOW…entific-writing/scripts/select_reporting_guidelines.py3CODE
LOW…/skills/scientific-writing/scripts/check_references.py3CODE
LOW…e/skills/scientific-writing/scripts/lint_manuscript.py3CODE
LOW.claude/skills/scientific-writing/scripts/_common.py3CODE
LOW…aude/skills/scientific-writing/scripts/audit_claims.py3CODE
LOW…skills/scientific-writing/scripts/validate_manifest.py3CODE
LOW…skills/scientific-writing/scripts/check_consistency.py3CODE
LOW…cal-decision-support/scripts/cohort_table_generator.py4CODE
LOW…cal-decision-support/scripts/evidence_profile_check.py4CODE
LOW…de/skills/clinical-decision-support/scripts/_common.py4CODE
LOW…decision-support/scripts/deidentification_checklist.py4CODE
LOW…ecision-support/scripts/decision_logic_traceability.py4CODE
LOW…decision-support/scripts/model_biomarker_evaluation.py4CODE
LOW…al-decision-support/scripts/survival_plan_validator.py4CODE
LOW…ical-decision-support/scripts/validate_cds_artifact.py4CODE
LOW…e/skills/literature-review/scripts/verify_citations.py11CODE
LOW…ills/scholar-evaluation/scripts/summarize_agreement.py4CODE
LOW…ude/skills/scholar-evaluation/scripts/check_process.py4CODE
LOW…scholar-evaluation/scripts/generate_report_scaffold.py4CODE
LOW…kills/scholar-evaluation/scripts/check_traceability.py4CODE
LOW…/skills/scholar-evaluation/scripts/calculate_scores.py4CODE
LOW.claude/skills/scholar-evaluation/scripts/_common.py4CODE
LOW…kills/scholar-evaluation/scripts/weight_sensitivity.py4CODE
LOW…e/skills/scholar-evaluation/scripts/validate_rubric.py4CODE
LOW…aude/skills/pptx/scripts/office/validators/__init__.py5CODE
288 more matches not shown…
Structural Annotation Overuse157 hits · 289 pts
SeverityFileLineSnippetContext
LOWCHANGELOG.md1041# Step 1: Identify topicsCOMMENT
LOWCHANGELOG.md1045# Step 2: Review/edit topics.txt manuallyCOMMENT
LOWCHANGELOG.md1047# Step 3: Research in parallelCOMMENT
LOW…skills/citation-management/references/core_workflow.md163#### Step 1: Scan for Incomplete EntriesCOMMENT
LOW…skills/citation-management/references/core_workflow.md178#### Step 2: Web Search for Missing MetadataCOMMENT
LOW…skills/citation-management/references/core_workflow.md232#### Step 3: Update BibTeX EntriesCOMMENT
LOW…skills/citation-management/references/core_workflow.md244#### Step 4: Handle Unfindable MetadataCOMMENT
LOW…/citation-management/references/citation_validation.md469### Step 1: Basic ValidationCOMMENT
LOW…/citation-management/references/citation_validation.md485### Step 2: Review ReportCOMMENT
LOW…/citation-management/references/citation_validation.md525### Step 3: Fix IssuesCOMMENT
LOW…/citation-management/references/citation_validation.md542### Step 4: Auto-FixCOMMENT
LOW…/citation-management/references/citation_validation.md565### Step 5: Manual ReviewCOMMENT
LOW…/citation-management/references/citation_validation.md576### Step 6: Re-ValidateCOMMENT
LOW…skills/citation-management/references/pubmed_search.md704 # Step 1: Basic searchCOMMENT
LOW…skills/citation-management/references/pubmed_search.md707 # Step 2: Add specificityCOMMENT
LOW…skills/citation-management/references/pubmed_search.md710 # Step 3: Add treatmentCOMMENT
LOW…skills/citation-management/references/pubmed_search.md713 # Step 4: Add study typeCOMMENT
LOW…skills/citation-management/references/pubmed_search.md717 # Step 5: Add date rangeCOMMENT
LOW…ls/citation-management/references/example_workflows.md11# Step 1: Find key papers on your topicCOMMENT
LOW…ls/citation-management/references/example_workflows.md22# Step 2: Extract metadata from search resultsCOMMENT
LOW…ls/citation-management/references/example_workflows.md31# Step 3: Add specific papers you already knowCOMMENT
LOW…ls/citation-management/references/example_workflows.md35# Step 4: Combine all BibTeX filesCOMMENT
LOW…ls/citation-management/references/example_workflows.md38# Step 5: Format and deduplicateCOMMENT
LOW…ls/citation-management/references/example_workflows.md45# Step 6: ValidateCOMMENT
LOW…ls/citation-management/references/example_workflows.md51# Step 7: Review any issuesCOMMENT
LOW…ls/citation-management/references/example_workflows.md54# Step 8: Use in LaTeXCOMMENT
LOW…ls/citation-management/references/example_workflows.md80# Step 1: Format and standardizeCOMMENT
LOW…ls/citation-management/references/example_workflows.md84# Step 2: Remove duplicatesCOMMENT
LOW…ls/citation-management/references/example_workflows.md89# Step 3: Validate and auto-fixCOMMENT
LOW…ls/citation-management/references/example_workflows.md94# Step 4: Sort by yearCOMMENT
LOW…ls/citation-management/references/example_workflows.md100# Step 5: Final validation reportCOMMENT
LOW…kills/citation-management/assets/citation_checklist.md73### Step 1: Format and CleanCOMMENT
LOW…kills/citation-management/assets/citation_checklist.md89### Step 2: ValidateCOMMENT
LOW…kills/citation-management/assets/citation_checklist.md105### Step 3: Review ReportCOMMENT
LOW…kills/citation-management/assets/citation_checklist.md116### Step 4: Final CheckCOMMENT
LOW.claude/skills/pdf/forms.md81## Step 1: Try Structure Extraction FirstCOMMENT
LOW.claude/skills/pdf/forms.md270## Step 2: Validate Before FillingCOMMENT
LOW.claude/skills/pdf/forms.md281## Step 3: Fill the FormCOMMENT
LOW.claude/skills/pdf/forms.md286## Step 4: Verify OutputCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md231### Step 0: MANDATORY Pre-Generation Review (DO THIS FIRST)COMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md259### Step 1: Plan Your Poster ElementsCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md270### Step 2: Generate Each Element (After Pre-Generation Review)COMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md353### Step 3: Assemble in LaTeX TemplateCOMMENT
LOW…cientific-slides/references/slide_design_principles.md726### Step 1: Define Visual IdentityCOMMENT
LOW…cientific-slides/references/slide_design_principles.md734### Step 2: Create Master TemplatesCOMMENT
LOW…cientific-slides/references/slide_design_principles.md744### Step 3: Apply ConsistentlyCOMMENT
LOW…cientific-slides/references/slide_design_principles.md753### Step 4: Review and RefineCOMMENT
LOW…entific-slides/references/data_visualization_slides.md548### Step 1: Start with High-Quality SourceCOMMENT
LOW…entific-slides/references/data_visualization_slides.md561### Step 2: Simplify for PresentationCOMMENT
LOW…entific-slides/references/data_visualization_slides.md577### Step 3: Optimize for ProjectionCOMMENT
LOW…entific-slides/references/data_visualization_slides.md592### Step 4: Add Context and AnnotationsCOMMENT
LOWextensions/docx-editor-zotero/EXAMPLES.md280# Step 1: PreviewCOMMENT
LOWextensions/docx-editor-zotero/EXAMPLES.md283# Step 2: First batch of deletionsCOMMENT
LOWextensions/docx-editor-zotero/EXAMPLES.md287# Step 3: ReorganizeCOMMENT
LOWextensions/docx-editor-zotero/EXAMPLES.md291# Step 4: Terminology updateCOMMENT
LOWextensions/docx-editor-zotero/EXAMPLES.md295# Step 5: Validate and saveCOMMENT
LOWcommands/scientific-writer-init.md24## Step 1: Check for Existing Instruction FilesCOMMENT
LOWcommands/scientific-writer-init.md39## Step 2: Locate the Template File PathsCOMMENT
LOWcommands/scientific-writer-init.md55## Step 3: Create or Update Each Instruction FileCOMMENT
LOWcommands/scientific-writer-init.md93## Step 4: Summarize What Was InstalledCOMMENT
97 more matches not shown…
Cross-Language Confusion40 hits · 202 pts
SeverityFileLineSnippetContext
HIGH…aude/skills/research-lookup/scripts/research_lookup.py126 "Find conflicting, contradictory, null, negative, replication, and limitation "CODE
HIGH.claude/skills/xlsx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH.claude/skills/xlsx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/xlsx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/xlsx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH.claude/skills/pptx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH.claude/skills/pptx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/pptx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/pptx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH.claude/skills/docx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH.claude/skills/docx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/docx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH.claude/skills/docx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGHscripts/bump_version.py333 print(f" 3. Commit changes: git add -A && git commit -m 'Bump version to {new_version}'")CODE
HIGHskills/research-lookup/scripts/research_lookup.py126 "Find conflicting, contradictory, null, negative, replication, and limitation "CODE
HIGHskills/xlsx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/xlsx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/xlsx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/pptx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/pptx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGHskills/docx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGHskills/docx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGHskills/docx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH…aude/skills/research-lookup/scripts/research_lookup.py126 "Find conflicting, contradictory, null, negative, replication, and limitation "CODE
HIGH…c_writer/.claude/skills/xlsx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH…c_writer/.claude/skills/xlsx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/xlsx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/xlsx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH…c_writer/.claude/skills/pptx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH…c_writer/.claude/skills/pptx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/pptx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/pptx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
HIGH…c_writer/.claude/skills/docx/scripts/office/soffice.py165 if (sv[0] >= 0 && sv[0] < 1024) {CODE
HIGH…c_writer/.claude/skills/docx/scripts/office/soffice.py184 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/docx/scripts/office/soffice.py193 if (sockfd >= 0 && sockfd < 1024 && is_shimmed[sockfd]) {CODE
HIGH…c_writer/.claude/skills/docx/scripts/office/soffice.py207 if (fd >= 0 && fd < 1024 && is_shimmed[fd]) {CODE
Decorative Section Separators28 hits · 99 pts
SeverityFileLineSnippetContext
MEDIUMtests/test_agent_plugin.py46# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py48# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py77# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py79# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py143# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py145# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py197# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py199# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py260# --------------------------------------------------------------------------COMMENT
MEDIUMtests/test_agent_plugin.py262# --------------------------------------------------------------------------COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py46 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py48 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py70 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py72 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py162 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py164 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py210 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py212 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py254 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py256 # ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py268# ===========================COMMENT
MEDIUMextensions/docx-editor-zotero/word_editor.py270# ===========================COMMENT
MEDIUMscripts/validate_agent_plugin.py117# ---------------------------------------------------------------------------COMMENT
MEDIUMscripts/validate_agent_plugin.py119# ---------------------------------------------------------------------------COMMENT
MEDIUMscripts/validate_agent_plugin.py303# ---------------------------------------------------------------------------COMMENT
MEDIUMscripts/validate_agent_plugin.py305# ---------------------------------------------------------------------------COMMENT
MEDIUMscripts/validate_agent_plugin.py444# ---------------------------------------------------------------------------COMMENT
MEDIUMscripts/validate_agent_plugin.py446# ---------------------------------------------------------------------------COMMENT
Modern AI Meta-Vocabulary27 hits · 81 pts
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MEDIUM.claude/skills/markitdown/references/workflows.md129## 5. RAG IngestionCOMMENT
MEDIUM…/skills/scholar-evaluation/references/local_tooling.md191## 7. Report scaffoldCOMMENT
MEDIUM.claude/skills/market-research-reports/SKILL.md140#### Measurement guardrailsCOMMENT
MEDIUM.claude/skills/venue-templates/SKILL.md143### Poster scaffoldCOMMENT
MEDIUM.claude/skills/venue-templates/SKILL.md209### Copy and customize a scaffoldCOMMENT
MEDIUM…ills/venue-templates/references/grants_requirements.md98### Bundled NSF scaffoldCOMMENT
MEDIUM…lls/hypothesis-generation/references/tool_reference.md210## 7. Preregistration scaffold generatorCOMMENT
MEDIUM…generation/assets/preregistration_scaffold_template.md1# Preregistration scaffold: {{PROJECT_ID}}COMMENT
MEDIUM.claude/skills/peer-review/references/tool_reference.md182## Review scaffold generatorCOMMENT
MEDIUMskills/markitdown/references/workflows.md129## 5. RAG IngestionCOMMENT
MEDIUMskills/scholar-evaluation/references/local_tooling.md191## 7. Report scaffoldCOMMENT
MEDIUMskills/market-research-reports/SKILL.md140#### Measurement guardrailsCOMMENT
MEDIUMskills/venue-templates/SKILL.md143### Poster scaffoldCOMMENT
MEDIUMskills/venue-templates/SKILL.md209### Copy and customize a scaffoldCOMMENT
MEDIUM…ills/venue-templates/references/grants_requirements.md98### Bundled NSF scaffoldCOMMENT
MEDIUM…lls/hypothesis-generation/references/tool_reference.md210## 7. Preregistration scaffold generatorCOMMENT
MEDIUM…generation/assets/preregistration_scaffold_template.md1# Preregistration scaffold: {{PROJECT_ID}}COMMENT
MEDIUMskills/peer-review/references/tool_reference.md182## Review scaffold generatorCOMMENT
MEDIUM…iter/.claude/skills/markitdown/references/workflows.md129## 5. RAG IngestionCOMMENT
MEDIUM…/skills/scholar-evaluation/references/local_tooling.md191## 7. Report scaffoldCOMMENT
MEDIUM…writer/.claude/skills/market-research-reports/SKILL.md140#### Measurement guardrailsCOMMENT
MEDIUM…entific_writer/.claude/skills/venue-templates/SKILL.md143### Poster scaffoldCOMMENT
MEDIUM…entific_writer/.claude/skills/venue-templates/SKILL.md209### Copy and customize a scaffoldCOMMENT
MEDIUM…ills/venue-templates/references/grants_requirements.md98### Bundled NSF scaffoldCOMMENT
MEDIUM…lls/hypothesis-generation/references/tool_reference.md210## 7. Preregistration scaffold generatorCOMMENT
MEDIUM…generation/assets/preregistration_scaffold_template.md1# Preregistration scaffold: {{PROJECT_ID}}COMMENT
MEDIUM…claude/skills/peer-review/references/tool_reference.md182## Review scaffold generatorCOMMENT
Redundant / Tautological Comments41 hits · 57 pts
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LOW…scientific-schematics/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…skills/citation-management/scripts/extract_metadata.py46 # Check if URLCOMMENT
LOW…s/citation-management/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…skills/infographics/scripts/generate_infographic_ai.py1164 # Check if quality is acceptableSTRING
LOW…lls/literature-review/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…laude/skills/literature-review/scripts/generate_pdf.py44 # Check if pandoc is installedCOMMENT
LOW…/skills/latex-posters/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW.claude/skills/latex-posters/scripts/review_poster.sh13# Check if file argument providedCOMMENT
LOW.claude/skills/latex-posters/scripts/review_poster.sh22# Check if file existsCOMMENT
LOW.claude/skills/latex-posters/scripts/review_poster.sh93 # Check if file is too large for emailCOMMENT
LOW…lls/scientific-slides/scripts/validate_presentation.py392 # Print resultsSTRING
LOW…lls/scientific-slides/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWscripts/publish.py239 # Check if tag already existsCOMMENT
LOW…scientific-schematics/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/citation-management/scripts/extract_metadata.py46 # Check if URLCOMMENT
LOW…s/citation-management/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/infographics/scripts/generate_infographic_ai.py1164 # Check if quality is acceptableSTRING
LOW…lls/literature-review/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/literature-review/scripts/generate_pdf.py44 # Check if pandoc is installedCOMMENT
LOWskills/latex-posters/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh13# Check if file argument providedCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh22# Check if file existsCOMMENT
LOWskills/latex-posters/scripts/review_poster.sh93 # Check if file is too large for emailCOMMENT
LOW…lls/scientific-slides/scripts/validate_presentation.py392 # Print resultsSTRING
LOW…lls/scientific-slides/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOWscientific_writer/core.py441 # Read the file from the zip and write it to the outputCOMMENT
LOWscientific_writer/cli.py238 # Check if user wants to start a new paperSTRING
LOWscientific_writer/utils.py114 # Check if user mentions continuation or search keywordsCOMMENT
LOWscientific_writer/utils.py128 # Check if topic words appear in user inputCOMMENT
LOW…scientific-schematics/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…skills/citation-management/scripts/extract_metadata.py46 # Check if URLCOMMENT
LOW…s/citation-management/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…skills/infographics/scripts/generate_infographic_ai.py1164 # Check if quality is acceptableSTRING
LOW…lls/literature-review/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…laude/skills/literature-review/scripts/generate_pdf.py44 # Check if pandoc is installedCOMMENT
LOW…/skills/latex-posters/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
LOW…/.claude/skills/latex-posters/scripts/review_poster.sh13# Check if file argument providedCOMMENT
LOW…/.claude/skills/latex-posters/scripts/review_poster.sh22# Check if file existsCOMMENT
LOW…/.claude/skills/latex-posters/scripts/review_poster.sh93 # Check if file is too large for emailCOMMENT
LOW…lls/scientific-slides/scripts/validate_presentation.py392 # Print resultsSTRING
LOW…lls/scientific-slides/scripts/generate_schematic_ai.py697 # Check if quality is acceptable - STOP EARLY if soCOMMENT
AI Slop Vocabulary15 hits · 45 pts
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MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/literature-review/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…/skills/latex-posters/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/scientific-slides/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/literature-review/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUMskills/latex-posters/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/scientific-slides/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…scientific-schematics/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…s/citation-management/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/literature-review/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…/skills/latex-posters/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
MEDIUM…lls/scientific-slides/scripts/generate_schematic_ai.py96 # Scientific diagram best practices prompt templateCOMMENT
Modern Structural Boilerplate25 hits · 25 pts
SeverityFileLineSnippetContext
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py10__all__ = [CODE
LOW.claude/skills/pptx/scripts/clean.py233def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None:CODE
LOW…aude/skills/pptx/scripts/office/validators/__init__.py10__all__ = [CODE
LOW.claude/skills/docx/scripts/accept_changes.py14logger = logging.getLogger(__name__)CODE
LOW…aude/skills/docx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWextensions/docx-editor-zotero/word_editor.py20logger = logging.getLogger(__name__)CODE
LOWextensions/docx-editor-zotero/zotero_docx_preserver.py41logger = logging.getLogger(__name__)CODE
LOWscripts/bump_version.py115def update_pyproject_version(pyproject_path: Path, new_version: str) -> None:CODE
LOWscripts/bump_version.py143def update_init_version(init_path: Path, new_version: str) -> None:CODE
LOWscripts/bump_version.py171def update_marketplace_version(marketplace_path: Path, new_version: str) -> None:CODE
LOWscripts/sync_skills.py283def update_hashes(data: dict[str, Any], root: Path) -> None:CODE
LOWskills/xlsx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWskills/pptx/scripts/clean.py233def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None:CODE
LOWskills/pptx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWskills/docx/scripts/accept_changes.py14logger = logging.getLogger(__name__)CODE
LOWskills/docx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWscientific_writer/__init__.py50__all__ = [CODE
LOWscientific_writer/core.py16logger = logging.getLogger(__name__)CODE
LOWscientific_writer/api.py37logger = logging.getLogger(__name__)CODE
LOWscientific_writer/utils.py9logger = logging.getLogger(__name__)CODE
LOW…aude/skills/xlsx/scripts/office/validators/__init__.py10__all__ = [CODE
LOWscientific_writer/.claude/skills/pptx/scripts/clean.py233def update_content_types(unpacked_dir: Path, removed_files: list[str]) -> None:CODE
LOW…aude/skills/pptx/scripts/office/validators/__init__.py10__all__ = [CODE
LOW…c_writer/.claude/skills/docx/scripts/accept_changes.py14logger = logging.getLogger(__name__)CODE
LOW…aude/skills/docx/scripts/office/validators/__init__.py10__all__ = [CODE
Over-Commented Block15 hits · 15 pts
SeverityFileLineSnippetContext
LOWpyproject.toml41Changelog = "https://github.com/K-Dense-AI/claude-scientific-writer/blob/main/CHANGELOG.md"COMMENT
LOWpyproject.toml141ignore-regex = '\b[a-z]+[A-Z]\w*\b|\b[A-Z][a-z]+[A-Z]\w*\b|\*\*.\*\*\w+|\\textbf\{.\}\w+'COMMENT
LOWpyproject.toml161# fallow - Gutenberg diagram layout term (fallow area)COMMENT
LOW…ls/citation-management/references/example_workflows.md61# You have a text file with DOIs (one per line)COMMENT
LOW…kills/literature-review/references/example_workflow.md41# - Use parallel-cli extract to fetch full content from promising URLsCOMMENT
LOW…ls/literature-review/references/database_strategies.md421# 2. Search bioRxivCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md281# Drug discovery workflow - HIGH-LEVEL ONLY, 3 stagesCOMMENT
LOW…ls/citation-management/references/example_workflows.md61# You have a text file with DOIs (one per line)COMMENT
LOWskills/literature-review/references/example_workflow.md41# - Use parallel-cli extract to fetch full content from promising URLsCOMMENT
LOW…ls/literature-review/references/database_strategies.md421# 2. Search bioRxivCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md281# Drug discovery workflow - HIGH-LEVEL ONLY, 3 stagesCOMMENT
LOW…ls/citation-management/references/example_workflows.md61# You have a text file with DOIs (one per line)COMMENT
LOW…kills/literature-review/references/example_workflow.md41# - Use parallel-cli extract to fetch full content from promising URLsCOMMENT
LOW…ls/literature-review/references/database_strategies.md421# 2. Search bioRxivCOMMENT
LOW…ls/latex-posters/references/ai_graphics_for_posters.md281# Drug discovery workflow - HIGH-LEVEL ONLY, 3 stagesCOMMENT
Fake / Example Data15 hits · 15 pts
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LOW…skills/pptx-posters/references/poster_content_guide.md158The validator rejects common placeholder forms such as TODO, TBD, Lorem ipsum,CODE
LOW…e/skills/scientific-writing/scripts/lint_manuscript.py24 re.compile(r"\blorem ipsum\b", re.IGNORECASE),CODE
LOW…-posters/references/compilation_and_quality_control.md270- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOW.claude/skills/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOW…kills/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOWskills/pptx-posters/references/poster_content_guide.md158The validator rejects common placeholder forms such as TODO, TBD, Lorem ipsum,CODE
LOWskills/scientific-writing/scripts/lint_manuscript.py24 re.compile(r"\blorem ipsum\b", re.IGNORECASE),CODE
LOW…-posters/references/compilation_and_quality_control.md270- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOWskills/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOWskills/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
LOW…skills/pptx-posters/references/poster_content_guide.md158The validator rejects common placeholder forms such as TODO, TBD, Lorem ipsum,CODE
LOW…e/skills/scientific-writing/scripts/lint_manuscript.py24 re.compile(r"\blorem ipsum\b", re.IGNORECASE),CODE
LOW…-posters/references/compilation_and_quality_control.md270- [ ] No placeholder text remaining (Lorem ipsum, TODO, etc.)CODE
LOW…/.claude/skills/latex-posters/scripts/review_poster.sh179echo " [ ] No placeholder text (Lorem ipsum, TODO, etc.)"CODE
LOW…kills/latex-posters/assets/poster_quality_checklist.md15- [ ] No placeholder text remaining (TODO, Lorem ipsum, etc.)CODE
Synthetic Comment Markers3 hits · 15 pts
SeverityFileLineSnippetContext
HIGH…ls/latex-posters/references/ai_graphics_for_posters.md80The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE
HIGH…ls/latex-posters/references/ai_graphics_for_posters.md80The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE
HIGH…ls/latex-posters/references/ai_graphics_for_posters.md80The #1 issue with AI-generated poster graphics is **TOO MUCH CONTENT**. This causes:CODE
Docstring Block Structure2 hits · 10 pts
SeverityFileLineSnippetContext
HIGHextensions/docx-editor-zotero/word_editor.py219 Validate and save the edited document Args: output_path: Path for output .docx STRING
HIGHscientific_writer/core.py201 Get the Anthropic API key. Args: api_key: Optional API key to use. If not provided, reads from environSTRING
AI Structural Patterns9 hits · 9 pts
SeverityFileLineSnippetContext
LOW…aude/skills/research-lookup/scripts/research_lookup.py143CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py1013CODE
LOWscripts/publish.py91CODE
LOWskills/research-lookup/scripts/research_lookup.py143CODE
LOWskills/infographics/scripts/generate_infographic_ai.py1013CODE
LOWscientific_writer/api.py62CODE
LOWscientific_writer/api.py695CODE
LOW…aude/skills/research-lookup/scripts/research_lookup.py143CODE
LOW…skills/infographics/scripts/generate_infographic_ai.py1013CODE