KANNA Workspace Notes

Secrets: use SOPS (secrets/global.enc.env or a per-project encrypted file). Avoid keeping config/secrets.json in git; .gitignore excludes it. Populate SEMANTIC_SCHOLAR_API_KEY (and any others) via scripts/load-secrets.sh before running tools.
Logs: transient writing/rag logs live under writing/*.log and logs/; they are ignored. Clean them freely.
Artifacts: large models/checkpoints are stored outside the repo in data/big-artifacts/academic-KANNA/... (see repo root README there). Keep new heavy files out of this tree.
Venvs and node_modules: intentionally absent; create per-session envs if needed.
If you add new configs, prefer YAML/JSON under config/ and document required env vars here.

Name		Name	Last commit message	Last commit date
Latest commit History 251 Commits
.claude		.claude
.githooks		.githooks
.github/workflows		.github/workflows
.qwen		.qwen
.serena		.serena
analysis		analysis
config		config
crossref_metadata		crossref_metadata
data		data
docs		docs
evaluation		evaluation
experiments/eval		experiments/eval
fresh sources		fresh sources
literature		literature
locate		locate
logs/rag_queries		logs/rag_queries
reports		reports
scripts		scripts
styles		styles
test_data		test_data
tools		tools
writing		writing
zotero-data		zotero-data
.gitattributes		.gitattributes
.gitignore		.gitignore
.mcp.json		.mcp.json
AGENTS.md		AGENTS.md
GEMINI.md		GEMINI.md
Makefile		Makefile
RAG_BUILD_VALIDATION_EXHAUSTIVE_REVIEW.md		RAG_BUILD_VALIDATION_EXHAUSTIVE_REVIEW.md
README.md		README.md
archive_list.txt		archive_list.txt
audit_duplicates.py		audit_duplicates.py
chap2-final-rich.pdf		chap2-final-rich.pdf
check_pdf_hashes.py		check_pdf_hashes.py
conftest.py		conftest.py
consolidate_pdfs.py		consolidate_pdfs.py
corpus_manifest.json		corpus_manifest.json
create_manifest.py		create_manifest.py
download_model.py		download_model.py
enrich_bib.py		enrich_bib.py
find_duplicates.py		find_duplicates.py
find_fuzzy_duplicates.py		find_fuzzy_duplicates.py
find_missing_bib_fields.py		find_missing_bib_fields.py
find_renamed_cells.py		find_renamed_cells.py
fpic_audit.jsonl		fpic_audit.jsonl
get_pdf_info.py		get_pdf_info.py
relink_bib.py		relink_bib.py

Provide feedback