Tree.clear()/reset() 不会清除或重新填充 _tree_nodes

`Tree.clear()` and `Tree.reset()` don't clear (or repopulate) the internal `_tree_nodes: dict[NodeID, TreeNode]` index, so `get_node_by_id()` can silently return a stale, discarded node after a `clear()`, and node IDs can collide with pre-clear entries.