feat: port template upgrades (citations, eval, chunking, nomic prefixes)

mcp 2.x is already on origin/main. This ports the rest of
docs-mcp-template #12–#16 without replacing HVM's BM25-first
search_docs path.

- Numbered [1] citations via docs_mcp/format.py
- Eval P@1 + JSONL sidecar + eval.pvalue
- Heading-recursive chunker, keep chunk-0 and MAX_CHARS=4000
- Nomic prefixes at embed time only; stored text unprefixed

Closes #15

rag/index.py

@@ -18,7 +18,7 @@ import chromadb
 from chromadb.config import Settings
 
 from .chunk import chunks_from_page
-from .embeddings import embedding_function
+from .embeddings import EMBED_DOC_PREFIX, embed_texts, embedding_function
 
 log = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO, format="%(asctime)s  %(message)s")
@@ -78,9 +78,12 @@ def upsert_to_chroma(records: list[dict]) -> int:
     total = 0
     for i in range(0, len(records), BATCH):
         chunk = records[i:i + BATCH]
+        texts = [r["text"] for r in chunk]
+        vectors = embed_texts(texts, prefix=EMBED_DOC_PREFIX, ef=embedding_function())
         col.upsert(
             ids=[r["id"] for r in chunk],
-            documents=[r["text"] for r in chunk],
+            documents=texts,
+            embeddings=vectors,
             metadatas=[r["metadata"] for r in chunk],
         )
         total += len(chunk)