docs: document JWT auth + frontend, flag dead V4 modules, fix stale repo claims - #2
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…epo claims
- New "Authentication" section: api/auth.py gates /rag/query and
/rag/stream behind a JWT bearer token via AUTH_ENABLED/JWT_SECRET,
same pattern as omnibioai-model-registry's require_auth. Not
previously documented anywhere. Practically important: omnibioai-
studio's deployed compose config sets AUTH_ENABLED=true, so the
README's own curl examples (no Authorization header) would 401
against the real deployment -- added a note on the example and a
full auth'd curl example in the new section.
- New "Frontend" section: omnibioai-dev-hub-ui/ (React+TS, Vite,
served at /_svc/devhub) is built into the same Dockerfile/image as
the API and exposed alongside it (EXPOSE 8082 5173) -- wasn't
mentioned anywhere, same gap found in omnibioai-control-center/
omnibioai-model-registry/omnibioai-workflow-bundles' own READMEs
this session.
- Repository Structure: added api/auth.py, api/middleware/trace.py
(real code, genuinely unwired -- not imported by main.py, no test
coverage), the frontend directory, and the rest of scripts/
(ingest.py, run_eval.py, check_and_reindex.sh -- only build_index.py
was listed).
- Flagged rag/query_router.py, tool_executor.py, memory_store.py (a
superseded "V4" agentic architecture -- 360 lines total, each with
its own test file, none imported by the live V6 engine or routes)
the same way this README already flags embeddings/embedder.py and
retrieval/retriever.py ("tests only, not live") -- they just hadn't
gotten the same treatment.
- Corrected "not present on disk" claims: omnibioai-security-audit and
omnibioai-hpc-policy-engine are annotated as skipped/missing in two
places (Current Index Stats, Supported Repositories), but both
directories exist on disk today. Reframed as a snapshot from
2026-06-14 rather than current fact, and added a staleness note to
the stats table itself (10,877 vectors / 17 of 19 repos) since a
rebuild today would almost certainly index both repos and produce
different numbers -- did not fabricate new numbers, since the local
faiss_index/ is empty and regenerating requires a live Ollama run.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
The core V6 RAG pipeline docs are accurate and well-maintained. The gaps are all in what's been added around it more recently.
Changes
api/auth.pygates/rag/queryand/rag/streambehind a JWT bearer token viaAUTH_ENABLED/JWT_SECRET, same pattern asomnibioai-model-registry'srequire_auth. Not previously documented anywhere. Practically important:omnibioai-studio's deployed compose config setsAUTH_ENABLED=true, so the README's own curl examples (noAuthorizationheader) would 401 against the real deployment — added a note on the example and a full auth'd curl example in the new section.omnibioai-dev-hub-ui/(React+TS, Vite, served at/_svc/devhub) is built into the sameDockerfile/image as the API and exposed alongside it (EXPOSE 8082 5173) — wasn't mentioned anywhere, same gap found inomnibioai-control-center/omnibioai-model-registry/omnibioai-workflow-bundles's own READMEs this session.api/auth.py,api/middleware/trace.py(real code, genuinely unwired — not imported bymain.py, no test coverage), the frontend directory, and the rest ofscripts/(ingest.py,run_eval.py,check_and_reindex.sh— onlybuild_index.pywas listed).rag/query_router.py,tool_executor.py,memory_store.py(a superseded "V4" agentic architecture — 360 lines total, each with its own test file, none imported by the live V6 engine or routes) the same way this README already flagsembeddings/embedder.pyandretrieval/retriever.py("tests only, not live") — they just hadn't gotten the same treatment.omnibioai-security-auditandomnibioai-hpc-policy-engineare annotated as skipped/missing in two places (Current Index Stats, Supported Repositories), but both directories exist on disk today. Reframed as a snapshot from 2026-06-14 rather than current fact, and added a staleness note to the stats table itself (10,877 vectors / 17 of 19 repos) — did not fabricate new numbers, since the localfaiss_index/is empty and regenerating requires a live Ollama run.Testing
Docs-only change. Verified against
api/auth.py,api/routes/rag.py,rag//retrieval/module imports,configs/repos.yaml,omnibioai-dev-hub-ui/vite.config.ts, theDockerfile, andomnibioai-studio's compose config — not against the prior README text.🤖 Generated with Claude Code