diff --git a/apps/api/src/api/v1/rag.py b/apps/api/src/api/v1/rag.py
index 6aa8b1bf4..26fb1fae9 100644
--- a/apps/api/src/api/v1/rag.py
+++ b/apps/api/src/api/v1/rag.py
@@ -87,15 +87,19 @@ async def _run_index() -> None:
     for source_dir in sources:
         if not source_dir.exists():
             continue
-        pattern = "*.md"
-        for md_file in source_dir.glob(pattern):
+        for md_file in source_dir.glob("*.md"):
             try:
-                count = await svc.index_document(
-                    file_path=md_file,
-                    source_type=source_dir.parts[0] if len(source_dir.parts) == 1 else source_dir.parts[1],
+                text = md_file.read_text(encoding="utf-8", errors="ignore")
+                source_type = source_dir.parts[-1]  # e.g. "runbooks", "adr", "skills"
+                ok = await svc.index_document(
+                    source=source_type,
+                    source_id=str(md_file),
+                    title=md_file.stem,
+                    text=text,
                 )
-                total += count
-                logger.debug("rag_indexed", file=str(md_file), chunks=count)
+                if ok:
+                    total += 1
+                logger.debug("rag_indexed", file=str(md_file))
             except Exception as e:
                 logger.warning("rag_index_file_failed", file=str(md_file), error=str(e))