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Which items do you mean? I think the sentence you are citing is about the rearranging the tabs in the editor pane. If you want to organize your docuemnts inside the project, it might be best for you to have a look at our screencast dedicated to just that topic.
Yes, you're right. You were talking about Stapler and I was some suffering from a weird kind of developer-question-blindess. Sorry for that. Here comes the right answer:
Stapler does allow dragging by pressing command only. And it's a flat hierarchy by intention. It is designed rather as a to-do list kind of thing than as an outliner. There are many good outliners out there, we did not want to create another one. And to be honest, we will not change that any time soon.
That said - there will be a completely new, completely different version of Stapler some day. The concept is pretty much done, the feature set will be amazing -- but for now we (sadly) do not have the time for it. But as far as I know, it will not add hierarchies in the first version...
The core of the concept of v2 will be the same like v1. A flat list, no easter eggs. But one new thing will be searching, better look, better support for attachments, and some things I don't want to talk about for now... As you can see with Ulysses, we've managed to get the app even less bloated than in the initial release over 6 years ago. We won't bloat stapler :)
We'll fix it on the website.
Maybe. Maybe not. ;)