This Package action will update an existing Application Tree, so you can replace an existing tree with your custom tree. Undo will revert the action. Blogpost describing the problem can be found here
Alias: UpdateAppTree
<Action runat="uninstall"
undo="false"
alias="UpdateAppTree"
treeAlias="media"
treeHandlerAssembly="umbraco"
treeHandlerType="loadMedia" />