.gitignore
CHANGELOG.md
LICENSE
README.md
ingest_test_ground_truth.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/pypi.yml
.windsurf/rules/bibliography-management.md
.windsurf/rules/git-workflow.md
.windsurf/rules/notes-convention.md
.windsurf/rules/source-figures.md
docs/tome-archive-v1.md
examples/config.yaml
patches/PR_DESCRIPTION.md
patches/README.md
patches/mcp_stdio_nonblocking.py
patches/stdio-nonblocking.patch
specs/get_quote-spec.md
src/tome/__init__.py
src/tome/__main__.py
src/tome/analysis.py
src/tome/bib.py
src/tome/call_log.py
src/tome/checksum.py
src/tome/chunk.py
src/tome/cite_tree.py
src/tome/config.py
src/tome/crossref.py
src/tome/errors.py
src/tome/extract.py
src/tome/figures.py
src/tome/file_meta.py
src/tome/filelock.py
src/tome/find_text.py
src/tome/git_diff.py
src/tome/grep_raw.py
src/tome/guide.py
src/tome/http.py
src/tome/identify.py
src/tome/index.py
src/tome/ingest.py
src/tome/issues.py
src/tome/latex.py
src/tome/manifest.py
src/tome/needful.py
src/tome/notes.py
src/tome/openalex.py
src/tome/paths.py
src/tome/py.typed
src/tome/rejected_dois.py
src/tome/s2ag.py
src/tome/s2ag_cli.py
src/tome/semantic_scholar.py
src/tome/server.py
src/tome/slug.py
src/tome/store.py
src/tome/summaries.py
src/tome/toc.py
src/tome/unpaywall.py
src/tome/validate.py
src/tome/validate_vault.py
src/tome/vault.py
src/tome/docs/configuration.md
src/tome/docs/directory-layout.md
src/tome/docs/document-analysis.md
src/tome/docs/exploration.md
src/tome/docs/getting-started.md
src/tome/docs/needful.md
src/tome/docs/notes.md
src/tome/docs/paper-workflow.md
src/tome/docs/reporting-issues.md
src/tome/docs/review-cycle.md
src/tome/docs/search.md
src/tome_mcp.egg-info/PKG-INFO
src/tome_mcp.egg-info/SOURCES.txt
src/tome_mcp.egg-info/dependency_links.txt
src/tome_mcp.egg-info/entry_points.txt
src/tome_mcp.egg-info/requires.txt
src/tome_mcp.egg-info/top_level.txt
tests/__init__.py
tests/conftest.py
tests/test_analysis.py
tests/test_bib.py
tests/test_checksum.py
tests/test_chunk.py
tests/test_chunk_semantic.py
tests/test_cite_tree.py
tests/test_concurrent_bib.py
tests/test_config.py
tests/test_crossref.py
tests/test_disambiguate_key.py
tests/test_discovery.py
tests/test_errors.py
tests/test_extract.py
tests/test_extract_enhanced.py
tests/test_figures.py
tests/test_file_meta.py
tests/test_filelock.py
tests/test_git_diff.py
tests/test_grep_raw.py
tests/test_guide.py
tests/test_http.py
tests/test_identify.py
tests/test_index.py
tests/test_ingest.py
tests/test_issues.py
tests/test_latex.py
tests/test_manifest.py
tests/test_needful.py
tests/test_notes.py
tests/test_openalex.py
tests/test_rejected_dois.py
tests/test_semantic_scholar.py
tests/test_server_routing.py
tests/test_slug.py
tests/test_store.py
tests/test_summaries.py
tests/test_toc.py
tests/test_unpaywall.py
tests/test_validate.py
tests/test_validate_vault.py
tests/test_vault.py