LICENSE
README.md
pyproject.toml
scriptorium/__init__.py
scriptorium/citations.py
scriptorium/cli.py
scriptorium/config.py
scriptorium/cowork.py
scriptorium/doctor.py
scriptorium/errors.py
scriptorium/export.py
scriptorium/extract.py
scriptorium/frontmatter.py
scriptorium/lock.py
scriptorium/migrate.py
scriptorium/nlm.py
scriptorium/paths.py
scriptorium/phase_state.py
scriptorium/prompts.py
scriptorium/publish.py
scriptorium/reviewers.py
scriptorium/scope.py
scriptorium/setup_flow.py
scriptorium/vault.py
scriptorium/fulltext/__init__.py
scriptorium/fulltext/arxiv.py
scriptorium/fulltext/cascade.py
scriptorium/fulltext/pdf_text.py
scriptorium/fulltext/pmc.py
scriptorium/fulltext/unpaywall.py
scriptorium/fulltext/user_pdf.py
scriptorium/mcp/__init__.py
scriptorium/mcp/__main__.py
scriptorium/mcp/server.py
scriptorium/obsidian/__init__.py
scriptorium/obsidian/queries.py
scriptorium/obsidian/stubs.py
scriptorium/overview/__init__.py
scriptorium/overview/generator.py
scriptorium/overview/linter.py
scriptorium/reasoning/__init__.py
scriptorium/reasoning/bib_export.py
scriptorium/reasoning/contradictions.py
scriptorium/reasoning/screening.py
scriptorium/reasoning/verify_citations.py
scriptorium/sources/__init__.py
scriptorium/sources/base.py
scriptorium/sources/openalex.py
scriptorium/sources/semantic_scholar.py
scriptorium/storage/__init__.py
scriptorium/storage/audit.py
scriptorium/storage/corpus.py
scriptorium/storage/evidence.py
scriptorium_cli.egg-info/PKG-INFO
scriptorium_cli.egg-info/SOURCES.txt
scriptorium_cli.egg-info/dependency_links.txt
scriptorium_cli.egg-info/entry_points.txt
scriptorium_cli.egg-info/requires.txt
scriptorium_cli.egg-info/top_level.txt
tests/test_arxiv.py
tests/test_audit.py
tests/test_audit_v03.py
tests/test_bib_export.py
tests/test_cascade.py
tests/test_cli.py
tests/test_cli_exit_codes.py
tests/test_cli_scope.py
tests/test_codex_symlinks.py
tests/test_command_lit_config.py
tests/test_command_lit_review.py
tests/test_command_skill_content.py
tests/test_commands_cc_only.py
tests/test_config.py
tests/test_config_load_order.py
tests/test_config_v03_keys.py
tests/test_conftest_publish_review.py
tests/test_contradictions.py
tests/test_corpus.py
tests/test_dataview_queries.py
tests/test_docs_cowork_smoke.py
tests/test_doctor.py
tests/test_e2e_caffeine.py
tests/test_e2e_lit_scoping.py
tests/test_end_of_review_prompt.py
tests/test_errors.py
tests/test_evidence.py
tests/test_export_citations.py
tests/test_export_code_fence_skip.py
tests/test_export_corpus_missing.py
tests/test_export_headings_paragraphs.py
tests/test_export_inline_formatting.py
tests/test_export_lists.py
tests/test_export_tables.py
tests/test_fixture_reviews.py
tests/test_frontmatter.py
tests/test_hook_evidence_gate.py
tests/test_hook_overview.py
tests/test_hook_scope_gate.py
tests/test_layer_a_hard_gates.py
tests/test_layer_a_injection.py
tests/test_layer_a_migration.py
tests/test_layer_a_phase_state.py
tests/test_layer_a_runtime_parity.py
tests/test_layer_b_extraction.py
tests/test_layer_b_override.py
tests/test_layer_b_reviewers.py
tests/test_layer_b_runtime_parity.py
tests/test_mcp_server.py
tests/test_migrate_review.py
tests/test_nlm_wrapper.py
tests/test_openalex.py
tests/test_overview_docx_failure_isolation.py
tests/test_overview_docx_opens.py
tests/test_overview_dual_write.py
tests/test_overview_generation.py
tests/test_overview_lint.py
tests/test_paper_stubs.py
tests/test_path_resolution.py
tests/test_paths.py
tests/test_paths_new_layout.py
tests/test_pdf_text.py
tests/test_plugin_layout.py
tests/test_plugin_manifest.py
tests/test_pmc.py
tests/test_preflight.py
tests/test_publish_audit.py
tests/test_publish_cli_flags.py
tests/test_publish_cowork.py
tests/test_publish_flow.py
tests/test_publish_idempotency.py
tests/test_publish_partial.py
tests/test_readme.py
tests/test_release_artifacts.py
tests/test_review_lock.py
tests/test_scope.py
tests/test_scope_audit.py
tests/test_screening.py
tests/test_semantic_scholar.py
tests/test_setup_init.py
tests/test_setup_state.py
tests/test_skill_configuring_scriptorium.py
tests/test_skill_generating_overview.py
tests/test_skill_lit_audit_trail.py
tests/test_skill_lit_contradiction_check.py
tests/test_skill_lit_extracting.py
tests/test_skill_lit_scoping.py
tests/test_skill_lit_screening.py
tests/test_skill_lit_searching.py
tests/test_skill_lit_synthesizing.py
tests/test_skill_publishing_to_notebooklm.py
tests/test_skill_running_lit_review.py
tests/test_skill_setting_up_scriptorium.py
tests/test_skill_using_scriptorium.py
tests/test_skill_v03_updates.py
tests/test_slash_publish_commands.py
tests/test_slash_setup.py
tests/test_sources_base.py
tests/test_unpaywall.py
tests/test_updated_commands.py
tests/test_user_pdf.py
tests/test_v04_release_docs.py
tests/test_vault_detection.py
tests/test_verify_citations.py
tests/test_verify_dual.py
tests/test_wikilink_parse.py
tests/test_write_failed_draft_location.py