LICENSE
README.md
pyproject.toml
lit_monitor/__init__.py
lit_monitor/cli.py
lit_monitor.egg-info/PKG-INFO
lit_monitor.egg-info/SOURCES.txt
lit_monitor.egg-info/dependency_links.txt
lit_monitor.egg-info/entry_points.txt
lit_monitor.egg-info/requires.txt
lit_monitor.egg-info/top_level.txt
lit_monitor/_data/__init__.py
lit_monitor/_data/item_routing.yaml
lit_monitor/_data/config/extraction_schema.yaml
lit_monitor/_data/config/review_schema.yaml
lit_monitor/_data/config/prompts/alias_consensus.example.yaml
lit_monitor/_data/config/prompts/ask_cypher.example.yaml
lit_monitor/_data/config/prompts/ask_summarize.example.yaml
lit_monitor/_data/config/prompts/cluster_naming.example.yaml
lit_monitor/_data/config/prompts/clustering.example.yaml
lit_monitor/_data/config/prompts/domain_extraction.example.yaml
lit_monitor/_data/config/prompts/extraction.example.yaml
lit_monitor/_data/config/prompts/long_tail_ner.example.yaml
lit_monitor/_data/config/prompts/query_expansion.example.yaml
lit_monitor/_data/config/prompts/rationale.example.yaml
lit_monitor/_data/config/prompts/re_extract_with_graph.example.yaml
lit_monitor/_data/config/prompts/relationship_extraction.example.yaml
lit_monitor/_data/config/prompts/synthesis.example.yaml
lit_monitor/_data/config_examples/concepts.example.yaml
lit_monitor/_data/config_examples/domain_context.example.yaml
lit_monitor/_data/config_examples/entity_aliases.example.yaml
lit_monitor/_data/config_examples/entity_types.example.yaml
lit_monitor/_data/config_examples/extraction.example.yaml
lit_monitor/_data/config_examples/paths.example.yaml
lit_monitor/_data/config_examples/predicates.example.yaml
lit_monitor/_data/config_examples/researchers.example.yaml
lit_monitor/_data/config_examples/topics.example.yaml
lit_monitor/_data/config_examples/examples/README.md
lit_monitor/_data/config_examples/examples/bioprocessing/concepts.yaml
lit_monitor/_data/config_examples/examples/bioprocessing/domain_context.yaml
lit_monitor/_data/config_examples/examples/bioprocessing/researchers.yaml
lit_monitor/_data/config_examples/examples/bioprocessing/topics.yaml
lit_monitor/_data/config_examples/examples/climate-science/concepts.yaml
lit_monitor/_data/config_examples/examples/climate-science/domain_context.yaml
lit_monitor/_data/config_examples/examples/climate-science/researchers.yaml
lit_monitor/_data/config_examples/examples/climate-science/topics.yaml
lit_monitor/_data/config_examples/examples/ml-research/concepts.yaml
lit_monitor/_data/config_examples/examples/ml-research/domain_context.yaml
lit_monitor/_data/config_examples/examples/ml-research/researchers.yaml
lit_monitor/_data/config_examples/examples/ml-research/topics.yaml
lit_monitor/_data/note_templates/discovery_digest.md.j2
lit_monitor/_data/note_templates/paper_note.md.j2
lit_monitor/_data/note_templates/synthesis_note.md.j2
lit_monitor/_vendor/README.md
lit_monitor/_vendor/__init__.py
lit_monitor/_vendor/findpapers/LICENSE
lit_monitor/_vendor/findpapers/__init__.py
lit_monitor/_vendor/findpapers/models/__init__.py
lit_monitor/_vendor/findpapers/models/paper.py
lit_monitor/_vendor/findpapers/models/publication.py
lit_monitor/_vendor/findpapers/models/search.py
lit_monitor/_vendor/findpapers/searchers/__init__.py
lit_monitor/_vendor/findpapers/searchers/acm_searcher.py
lit_monitor/_vendor/findpapers/searchers/arxiv_searcher.py
lit_monitor/_vendor/findpapers/searchers/biorxiv_searcher.py
lit_monitor/_vendor/findpapers/searchers/ieee_searcher.py
lit_monitor/_vendor/findpapers/searchers/medrxiv_searcher.py
lit_monitor/_vendor/findpapers/searchers/pubmed_searcher.py
lit_monitor/_vendor/findpapers/searchers/rxiv_searcher.py
lit_monitor/_vendor/findpapers/searchers/scopus_searcher.py
lit_monitor/_vendor/findpapers/tools/__init__.py
lit_monitor/_vendor/findpapers/tools/bibtex_generator_tool.py
lit_monitor/_vendor/findpapers/tools/downloader_tool.py
lit_monitor/_vendor/findpapers/tools/refiner_tool.py
lit_monitor/_vendor/findpapers/tools/search_runner_tool.py
lit_monitor/_vendor/findpapers/utils/common_util.py
lit_monitor/_vendor/findpapers/utils/persistence_util.py
lit_monitor/_vendor/findpapers/utils/publication_util.py
lit_monitor/_vendor/findpapers/utils/query_util.py
lit_monitor/_vendor/findpapers/utils/requests_util.py
lit_monitor/api/__init__.py
lit_monitor/api/insights.py
lit_monitor/api/queries.py
lit_monitor/clustering/__init__.py
lit_monitor/clustering/assign.py
lit_monitor/clustering/atrophy.py
lit_monitor/clustering/exploration.py
lit_monitor/clustering/kmeans.py
lit_monitor/clustering/naming.py
lit_monitor/clustering/recompute.py
lit_monitor/clustering/write_back.py
lit_monitor/core/__init__.py
lit_monitor/core/atomic_write.py
lit_monitor/core/chunker.py
lit_monitor/core/config.py
lit_monitor/core/config_schema.py
lit_monitor/core/doi.py
lit_monitor/core/doi_resolver.py
lit_monitor/core/http_client.py
lit_monitor/core/item_router.py
lit_monitor/core/markdown_processor.py
lit_monitor/core/path_utils.py
lit_monitor/core/seed.py
lit_monitor/core/state_db.py
lit_monitor/core/strict_mode.py
lit_monitor/core/zotero_client.py
lit_monitor/domain/__init__.py
lit_monitor/domain/extract.py
lit_monitor/eval/__init__.py
lit_monitor/eval/quality_check.py
lit_monitor/graph/__init__.py
lit_monitor/graph/aliases.py
lit_monitor/graph/ask.py
lit_monitor/graph/backfill.py
lit_monitor/graph/db.py
lit_monitor/graph/entity_extractor.py
lit_monitor/graph/import_citations.py
lit_monitor/graph/long_tail.py
lit_monitor/graph/migrations.py
lit_monitor/graph/ner.py
lit_monitor/graph/ner_pipeline.py
lit_monitor/graph/normalizer.py
lit_monitor/graph/propose_aliases.py
lit_monitor/graph/query_expansion.py
lit_monitor/graph/relationship_extractor.py
lit_monitor/graph/relationship_llm.py
lit_monitor/graph/relationship_validator.py
lit_monitor/graph/schema_describer.py
lit_monitor/graph/trending.py
lit_monitor/graph/vocab.py
lit_monitor/learning/__init__.py
lit_monitor/learning/ranking.py
lit_monitor/learning/rocchio.py
lit_monitor/llm/__init__.py
lit_monitor/llm/embedding_client.py
lit_monitor/llm/extraction_schema.py
lit_monitor/llm/extractor.py
lit_monitor/llm/llm_client.py
lit_monitor/llm/prompt_registry.py
lit_monitor/llm/prompt_safety.py
lit_monitor/llm/ranker.py
lit_monitor/llm/token_budget.py
lit_monitor/mcp/__init__.py
lit_monitor/mcp/cypher_guard.py
lit_monitor/mcp/graph_server.py
lit_monitor/mcp/tools.py
lit_monitor/notify/__init__.py
lit_monitor/notify/os_notification.py
lit_monitor/obsidian_tools/__init__.py
lit_monitor/obsidian_tools/re_extract.py
lit_monitor/obsidian_tools/relink.py
lit_monitor/obsidian_tools/rerender.py
lit_monitor/obsidian_tools/retheme.py
lit_monitor/obsidian_tools/save_answer.py
lit_monitor/obsidian_tools/sync.py
lit_monitor/obsidian_tools/synthesize.py
lit_monitor/output/__init__.py
lit_monitor/output/digest_renderer.py
lit_monitor/output/embeddings.py
lit_monitor/output/obsidian_writer.py
lit_monitor/output/reranker.py
lit_monitor/pipelines/__init__.py
lit_monitor/pipelines/_ingest.py
lit_monitor/pipelines/brain_build.py
lit_monitor/pipelines/chunks_backfill.py
lit_monitor/pipelines/discovery.py
lit_monitor/pipelines/embeddings_migration.py
lit_monitor/pipelines/model_compare.py
lit_monitor/retrieval/__init__.py
lit_monitor/retrieval/branch.py
lit_monitor/retrieval/rrf.py
lit_monitor/search/__init__.py
lit_monitor/search/_constants.py
lit_monitor/search/citation_graph.py
lit_monitor/search/researcher_tracker.py
lit_monitor/search/search_runner.py
lit_monitor/search/semantic_scholar.py
lit_monitor/server/__init__.py
lit_monitor/server/app.py
lit_monitor/server/config_io.py
lit_monitor/server/csrf.py
lit_monitor/server/dev_sandbox.py
lit_monitor/server/runtime.py
lit_monitor/server/scheduler.py
lit_monitor/server/routes/__init__.py
lit_monitor/server/routes/ask.py
lit_monitor/server/routes/brain_build.py
lit_monitor/server/routes/control.py
lit_monitor/server/routes/corpus.py
lit_monitor/server/routes/dev.py
lit_monitor/server/routes/discovery.py
lit_monitor/server/routes/discovery_notify.py
lit_monitor/server/routes/domain.py
lit_monitor/server/routes/entities.py
lit_monitor/server/routes/feedback.py
lit_monitor/server/routes/fs.py
lit_monitor/server/routes/graph.py
lit_monitor/server/routes/health.py
lit_monitor/server/routes/ingest.py
lit_monitor/server/routes/papers.py
lit_monitor/server/routes/query.py
lit_monitor/server/routes/schedule.py
lit_monitor/server/routes/search.py
lit_monitor/server/routes/settings.py
lit_monitor/server/routes/setup.py
lit_monitor/server/routes/sse.py
lit_monitor/server/routes/themes.py
lit_monitor/server/routes/topics.py
lit_monitor/server/routes/trending.py
lit_monitor/server/routes/zotero.py
lit_monitor/server/scheduler_templates/launchd.plist.j2
lit_monitor/server/scheduler_templates/systemd.service.j2
lit_monitor/server/scheduler_templates/systemd.timer.j2
lit_monitor/server/static/site.css
lit_monitor/server/static/site.js
lit_monitor/server/static/js/feedback.js
lit_monitor/server/templates/base.html
lit_monitor/server/templates/index.html
lit_monitor/server/templates/_partials/paper_card.html
lit_monitor/server/templates/_partials/score_decomposition.html
lit_monitor/server/templates/ask/_answer.html
lit_monitor/server/templates/ask/_cypher_result.html
lit_monitor/server/templates/ask/_saved.html
lit_monitor/server/templates/ask/_table.html
lit_monitor/server/templates/ask/index.html
lit_monitor/server/templates/brain_build/_controls.html
lit_monitor/server/templates/brain_build/index.html
lit_monitor/server/templates/corpus/_graph.html
lit_monitor/server/templates/corpus/_related.html
lit_monitor/server/templates/corpus/_table.html
lit_monitor/server/templates/corpus/detail.html
lit_monitor/server/templates/corpus/index.html
lit_monitor/server/templates/dev/index.html
lit_monitor/server/templates/discovery/_controls.html
lit_monitor/server/templates/discovery/chooser.html
lit_monitor/server/templates/discovery/index.html
lit_monitor/server/templates/discovery/run_detail.html
lit_monitor/server/templates/domain/index.html
lit_monitor/server/templates/graph/_overview.html
lit_monitor/server/templates/graph/index.html
lit_monitor/server/templates/insights/_timeline.html
lit_monitor/server/templates/insights/_top_papers.html
lit_monitor/server/templates/insights/index.html
lit_monitor/server/templates/schedule/index.html
lit_monitor/server/templates/settings/index.html
lit_monitor/server/templates/setup/_base.html
lit_monitor/server/templates/setup/_concepts_progress.html
lit_monitor/server/templates/setup/_credentials_result.html
lit_monitor/server/templates/setup/_domain_result.html
lit_monitor/server/templates/setup/_extraction_result.html
lit_monitor/server/templates/setup/_fs_modal.html
lit_monitor/server/templates/setup/_paths_result.html
lit_monitor/server/templates/setup/_researchers_result.html
lit_monitor/server/templates/setup/_researchers_row.html
lit_monitor/server/templates/setup/_routing_result.html
lit_monitor/server/templates/setup/_topics_result.html
lit_monitor/server/templates/setup/_topics_row.html
lit_monitor/server/templates/setup/complete.html
lit_monitor/server/templates/setup/index.html
lit_monitor/server/templates/setup/step_concepts.html
lit_monitor/server/templates/setup/step_credentials.html
lit_monitor/server/templates/setup/step_domain.html
lit_monitor/server/templates/setup/step_extraction.html
lit_monitor/server/templates/setup/step_paths.html
lit_monitor/server/templates/setup/step_researchers.html
lit_monitor/server/templates/setup/step_routing.html
lit_monitor/server/templates/setup/step_topics.html
lit_monitor/server/templates/themes/detail.html
lit_monitor/server/templates/themes/index.html
lit_monitor/server/templates/trending/index.html
lit_monitor/setup/__init__.py
lit_monitor/setup/_paths.py
lit_monitor/setup/check_configured.py
lit_monitor/setup/check_graph.py
lit_monitor/setup/check_ollama.py
lit_monitor/setup/check_vault.py
lit_monitor/setup/check_zotero.py
lit_monitor/setup/diagnose.py
lit_monitor/setup/health_check.py
lit_monitor/setup/reset.py
lit_monitor/vocabulary/__init__.py
lit_monitor/vocabulary/clusterer.py
lit_monitor/vocabulary/keyword_extractor.py
lit_monitor/vocabulary/normalizer.py
lit_monitor/vocabulary/topic_merger.py