core/agent: shift persist_from when prepending system prompt

src/plyngent/agent/chat.py

@@ -210,9 +210,9 @@ class ChatAgent:
         if self.messages and isinstance(self.messages[0], SystemChatMessage):
             return
         self.messages.insert(0, SystemChatMessage(content=self.system_prompt))
-        # System inject is not a DB message unless already stored.
+        # Prepended system is local-only; shift the checkpoint so indices that
-        if self._persist_from == 0:
+        # already pointed past stored messages stay correct after insert.
-            self._persist_from = 1
+        self._persist_from = min(len(self.messages), self._persist_from + 1)
 
     def replace_messages(
         self,

tests/test_cli/test_compact_cmd.py

@@ -152,10 +152,15 @@ async def test_rebuild_client_preserves_persist_cursor(tmp_path: Path) -> None:
             [UserChatMessage(content="hi"), AssistantChatMessage(content="yo")],
             persisted=True,
         )
-        assert state.agent.persist_from == 2
+        # Default system prompt is prepended locally (not a DB row); checkpoint
+        # shifts so the two stored turns stay in the persisted prefix.
+        n_msgs = len(state.agent.messages)
+        assert n_msgs >= 2
+        assert state.agent.persist_from == n_msgs
+        cursor = state.agent.persist_from
         state.rebuild_client()
-        assert len(state.agent.messages) == 2
+        assert len(state.agent.messages) == n_msgs
-        assert state.agent.persist_from == 2
+        assert state.agent.persist_from == cursor
     finally:
         await memory.close()