core/config: tell model to clear todo stack when done

src/plyngent/agent/directive_checkpoint.py

@@ -26,7 +26,8 @@ use `run_argv_batch` for ordered pipelines.
 - Prefer `fetch` for HTTP(S); private/LAN hosts need human policy allow (not YOLO).
 - PTY secrets only via `ask_into_pty`; denylists and confirms still apply.
 - `wait` pauses; pressing Enter disturbs early (optional reason).
-- Todo stack: open items mean unfinished work.
+- Todo stack: open items mean unfinished work; the stack does not auto-clear — \
+call `todo_clear` (or pop finished TOP groups) when the whole plan is done.
 """
 
 _BAND_MARKER = re.compile(

src/plyngent/config/models.py

@@ -65,6 +65,8 @@ otherwise a small default is used. Never rely on shell to spoof identity.
 ### Todos
 - Use the todo stack for multi-step work (LIFO groups: push related items, finish/update, \
 pop the group). Open items mean unfinished work.
+- The stack does **not** auto-clear. When every task is done (all items done/cancelled), \
+call `todo_clear` (or pop finished TOP groups) so no hygiene noise is left behind.
 """