Merge branch 'wip/oie-pipeline-eval-harness' into exp/dual-index-and-name-packer

Sync with PR #1088 upstream. Prefer dual-index librarian defaults on
conflicts; take 1088-only harness/full-pipeline/NIST/harvester additions.

Author: northdpole

.env.example

@@ -52,14 +52,25 @@ GOOGLE_CLIENT_SECRET=your-client-secret
 GOOGLE_SECRET_JSON=path/to/secret.json
 LOGIN_ALLOWED_DOMAINS=example.com
 
-# GCP
+# GCP / Gemini (optional — any LiteLLM provider works for Module B)
 
 GCP_NATIVE=false
 GEMINI_API_KEY=your-gemini-api-key
 VERTEX_CHAT_MODEL=gemini-2.5-flash
 VERTEX_EMBED_CONTENT_MODEL=gemini-embedding-001
 
-# Noise / Relevance Filter (Module B)
+# Other chat providers (LiteLLM). Set the key that matches CRE_NOISE_FILTER_LLM_MODEL.
+# OPENAI_API_KEY=sk-...
+# ANTHROPIC_API_KEY=sk-ant-...
+# GROQ_API_KEY=gsk_...
+# MISTRAL_API_KEY=...
+# OPENROUTER_API_KEY=...
+
+# Noise / Relevance Filter (Module B) — LiteLLM model id (provider/model)
+# Examples: gemini/gemini-2.5-flash-lite | openai/gpt-4o-mini |
+#           anthropic/claude-haiku-4-5 | groq/llama-3.3-70b-versatile
+# Any chat model LiteLLM supports; mid-size models usually work best
+# (cheap + reliable for this classify gate — avoid tiny completion stubs).
 
 CRE_NOISE_FILTER_LLM_MODEL=gemini/gemini-2.5-flash-lite
 CRE_NOISE_FILTER_BATCH_SIZE=10

.gitignore

@@ -79,6 +79,8 @@ standards_cache.sqlite
 !docs/gsoc_2026_module_b/module_c_contract.md
 !docs/gsoc_2026_module_b/module_b_runbook.md
 !docs/gsoc_2026_module_b/final_metrics.md
+!docs/oie/*.md
+!scripts/oie_owasp_eval/experiments/*.md
 
 ### Dev DBDumps
 *.sql

application/cmd/cre_main.py

@@ -911,6 +911,25 @@ def run(args: argparse.Namespace) -> None:  # pragma: no cover
             sys.exit(1)
         return
 
+    if str(getattr(args, "ingest_github", "") or "").strip():
+        import sys
+
+        from application import sqla
+        from application.utils.harvester.github_url_ingest import ingest_github_url
+
+        db_connect(args.cache_file)
+        counts = ingest_github_url(
+            str(args.ingest_github).strip(),
+            session=sqla.session,
+            cache_file=args.cache_file,
+            branch_override=(getattr(args, "ingest_branch", "") or "").strip() or None,
+            keep_all=bool(getattr(args, "ingest_keep_all", False)),
+            model_override=(getattr(args, "ingest_model", "") or "").strip() or None,
+        )
+        if counts.errors or (counts.knowledge + counts.uncertain) == 0:
+            sys.exit(1)
+        return
+
     if getattr(args, "run_noise_filter", False):
         import sys