fix(spec): prefer linked agent todo on session sync pull.

Stale per-session todo.txt no longer overwrites merged tasks_md after workspace import-agent-plan.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: agentpike

cecli/spec/agent_todos.py

@@ -479,6 +479,29 @@ def session_agent_todo_relpath(session: AgentTodoSession) -> str:
     return session.coder.local_agent_folder("todo.txt")
 
 
+def _resolve_agent_todo_pull_relpath(
+    api: WorkspaceTodos,
+    store: TodoStore,
+    session: AgentTodoSession,
+) -> str:
+    """Prefer the active task's linked agent todo over this session's stale copy."""
+    session_relpath = session_agent_todo_relpath(session)
+    active = api.find(store, store.active_id) if store.active_id else None
+    if active:
+        linked = parse_agent_todo_link(active.links)
+        if linked:
+            linked_path = api.root / linked
+            if linked_path.is_file():
+                return linked.replace("\\", "/")
+    session_path = api.root / session_relpath
+    if session_path.is_file():
+        return session_relpath
+    latest = find_latest_agent_todo_txt(api.root)
+    if latest:
+        return str(latest.relative_to(api.root)).replace("\\", "/")
+    return session_relpath
+
+
 def try_import_agent_plan_for_workspace(
     workspace_dir: str | Path,
     *,
@@ -507,12 +530,13 @@ def sync_session_agent_todos(
     Returns ``(store, sanitize_warnings)``.
     """
     api = WorkspaceTodos(session.coder.root)
-    relpath = session_agent_todo_relpath(session)
+    session_relpath = session_agent_todo_relpath(session)
     store = api.load()
     warnings: list[str] = []
 
     if pull:
-        path = api.root / relpath
+        pull_relpath = _resolve_agent_todo_pull_relpath(api, store, session)
+        path = api.root / pull_relpath
         if path.is_file():
             rows = parse_agent_todo_txt(path.read_text(encoding="utf-8"))
             if rows and sanitize is not None:
@@ -528,14 +552,14 @@ def sync_session_agent_todos(
                     store,
                     rows,
                     target_todo_id=store.active_id,
-                    agent_todo_relpath=relpath,
+                    agent_todo_relpath=pull_relpath,
                 )
 
     if push_active and store.active_id:
         item = api.find(store, store.active_id)
         if item:
-            export_todo_item_to_agent(api.root, relpath, item)
-            _ensure_agent_link(item, relpath)
+            export_todo_item_to_agent(api.root, session_relpath, item)
+            _ensure_agent_link(item, session_relpath)
             item.updated_at = _now_iso()
 
     api.save(store)

tests/spec/test_agent_todos.py

@@ -22,6 +22,7 @@
     rows_from_todo_item,
     rows_to_tasks_md,
     sanitize_agent_todo_rows,
+    sync_session_agent_todos,
 )
 from cecli.spec.todos import ChecklistItem, TodoItem, WorkspaceTodos, _now_iso
 
@@ -267,3 +268,58 @@ def test_load_agent_todo_rows_from_latest(tmp_path: Path):
     assert len(rows) == 1
     assert rows[0].current
     assert "3.1" in rows[0].text
+
+
+def test_sync_session_pull_prefers_linked_agent_todo_over_stale_session_copy(tmp_path: Path):
+    """Pre-session push must not revert a later workspace import from the linked todo.txt."""
+    spec_tasks = (
+        "## Implementation tasks\n\n"
+        "- [ ] 1. Wire generate-spec API for REQ-001 (depends: none)\n"
+        "- [ ] 2. Add tests for REQ-002 (depends: 1)\n"
+    )
+    api = WorkspaceTodos(tmp_path)
+    store = api.load()
+    item = TodoItem(
+        id="user1",
+        title="My feature",
+        tasks_md=spec_tasks,
+        status="in_progress",
+        links=[],
+        checklist=[],
+        created_at=_now_iso(),
+        updated_at=_now_iso(),
+    )
+    store.todos.append(item)
+    store.active_id = item.id
+    api.save(store)
+
+    class FakeCoder:
+        def __init__(self, root: Path):
+            self.root = root
+
+        def local_agent_folder(self, name: str) -> str:
+            return f".cecli/agents/2026-06-03/session-a/{name}"
+
+    class FakeSession:
+        def __init__(self, root: Path):
+            self.coder = FakeCoder(root)
+
+    session_rel = ".cecli/agents/2026-06-03/session-a/todo.txt"
+    export_todo_item_to_agent(tmp_path, session_rel, item)
+
+    linked_rel = ".cecli/agents/2026-05-27/imported/todo.txt"
+    linked = tmp_path / linked_rel
+    linked.parent.mkdir(parents=True)
+    linked.write_text(
+        "Done:\n"
+        "✓ 1. Wire generate-spec API for REQ-001 (depends: none)\n\n"
+        "Remaining:\n"
+        "→ 2. Add tests for REQ-002 (depends: 1)\n",
+        encoding="utf-8",
+    )
+    import_agent_plan_for_workspace(tmp_path, agent_todo_relpath=linked_rel)
+
+    store2, _ = sync_session_agent_todos(FakeSession(tmp_path), pull=True, push_active=True)
+    merged = store2.todos[0]
+    assert "- [x] 1. Wire generate-spec" in merged.tasks_md
+    assert merged.checklist[0].done is True