client.ask routes through the rag skill; always show citations in CLI

haiku_rag_slim/haiku/rag/app.py

@@ -443,14 +443,12 @@ class HaikuRAGApp:  # pragma: no cover
     async def ask(
         self,
         question: str,
-        cite: bool = False,
         filter: str | None = None,
     ):
         """Ask a question using the RAG system.
 
         Args:
             question: The question to ask
-            cite: Include citations in the answer
             filter: SQL WHERE clause to filter documents
         """
         async with HaikuRAG(
@@ -465,9 +463,8 @@ class HaikuRAGApp:  # pragma: no cover
             self.console.print()
             self.console.print("[bold green]Answer:[/bold green]")
             self.console.print(Markdown(answer))
-            if cite and citations:
-                for renderable in format_citations_rich(citations):
-                    self.console.print(renderable)
+            for renderable in format_citations_rich(citations):
+                self.console.print(renderable)
 
     async def analyze(
         self,

haiku_rag_slim/haiku/rag/cli.py

@@ -369,11 +369,6 @@ def ask(  # pragma: no cover
         "--db",
         help="Path to the LanceDB database file",
     ),
-    cite: bool = typer.Option(
-        False,
-        "--cite",
-        help="Include citations in the response",
-    ),
     filter: str | None = typer.Option(
         None,
         "--filter",
@@ -385,7 +380,6 @@ def ask(  # pragma: no cover
     asyncio.run(
         app.ask(
             question=question,
-            cite=cite,
             filter=filter,
         )
     )

haiku_rag_slim/haiku/rag/client/__init__.py

@@ -368,12 +368,11 @@ class HaikuRAG:
     async def ask(
         self,
         question: str,
-        system_prompt: str | None = None,
         filter: str | None = None,
     ) -> "tuple[str, list[Citation]]":
         from haiku.rag.client.agents import ask
 
-        return await ask(self, question, system_prompt, filter)
+        return await ask(self, question, filter)
 
     async def research(
         self,

haiku_rag_slim/haiku/rag/client/agents.py

@@ -9,24 +9,32 @@ if TYPE_CHECKING:
 async def ask(
     client: "HaikuRAG",
     question: str,
-    system_prompt: str | None = None,
     filter: str | None = None,
 ) -> "tuple[str, list[Citation]]":
-    """Ask a question using the configured QA agent.
+    """Ask a question against the knowledge base via the rag skill.
 
     Args:
         client: The HaikuRAG client.
         question: The question to ask.
-        system_prompt: Optional custom system prompt for the QA agent.
         filter: SQL WHERE clause to filter documents.
 
     Returns:
         Tuple of (answer text, list of resolved citations).
     """
-    from haiku.rag.agents.qa import get_qa_agent
+    from haiku.rag.skills.rag import RAGState, create_skill
+    from haiku.rag.utils import get_model
+    from haiku.skills import run_skill
 
-    qa_agent = get_qa_agent(client, config=client._config, system_prompt=system_prompt)
-    return await qa_agent.answer(question, filter=filter)
+    skill = create_skill(db_path=client.store.db_path, config=client._config)
+    state = RAGState(document_filter=filter)
+    model = get_model(client._config.qa.model, client._config)
+    answer, _, _ = await run_skill(model, skill, question, state=state)
+    citations = [
+        state.citation_index[cid]
+        for cid in state.citations
+        if cid in state.citation_index
+    ]
+    return answer, citations
 
 
 async def research(