feat: citations, eval sidecar/pvalue/trace, nomic prefixes

mcp 2.x already on main. Does not replace the variety chunker
(one chunk per variety is the anti-hallucination contract).

- Numbered [1] citations on search_docs / search_trials
- Eval JSONL sidecar, k-curve, eval.pvalue, eval.trace
- Nomic prefixes at embed time only; stored text unprefixed

Closes #25

rag/test_embeddings.py

@@ -0,0 +1,41 @@
+"""Prefix helpers — no Ollama, no Chroma."""
+from __future__ import annotations
+
+import unittest
+
+from rag.embeddings import apply_prefix, embed_texts
+
+
+class FakeEmbedder:
+    def __init__(self) -> None:
+        self.seen: list[str] = []
+
+    def __call__(self, texts: list[str]) -> list[list[float]]:
+        self.seen.extend(texts)
+        return [[0.0, 1.0] for _ in texts]
+
+
+class PrefixTests(unittest.TestCase):
+    def test_index_sends_doc_prefix_keeps_raw_text(self) -> None:
+        fake = FakeEmbedder()
+        raw = ["hello"]
+        vecs = embed_texts(raw, prefix="search_document: ", ef=fake)
+        self.assertEqual(fake.seen, ["search_document: hello"])
+        self.assertEqual(raw, ["hello"])  # caller storage unchanged
+        self.assertEqual(len(vecs), 1)
+
+    def test_query_sends_query_prefix(self) -> None:
+        fake = FakeEmbedder()
+        embed_texts(["q"], prefix="search_query: ", ef=fake)
+        self.assertEqual(fake.seen, ["search_query: q"])
+        self.assertNotIn("q", fake.seen)
+
+    def test_empty_prefix_is_raw(self) -> None:
+        self.assertEqual(apply_prefix("hello", ""), "hello")
+        fake = FakeEmbedder()
+        embed_texts(["hello"], prefix="", ef=fake)
+        self.assertEqual(fake.seen, ["hello"])
+
+
+if __name__ == "__main__":
+    unittest.main()