will the hierarchy structure in DT 2.0 be upgraded? I am thinking specifically of files being able to be hierarchically ‘under’ other files. This makes note-taking of, say, PDF essays or audio or movie clips, easier and much nicer in that the notes can hierarchically sit underneath the files they are connected to.
The application Mori has this type of structure and it would be really cool to have in DT 2.0
Actually, yuck. I actually sorta don’t like this about Mori. And if you can file stuff under files… how can you remember where things go?
Conceptually, folders hold things (either files or other folders). Files… are files.
The point is not that you have to put files under other files, but that you can. Mori doesn’t force you to do this.
I would mention omnioutliner as well, since it is the same there (which I think Mori patterns itself after somwhat) and it is a standout feature there as well.
If it was implemented, you would not need to change anything in the way you do things, it would just be there for those who do. I think it is ‘yuck’ that I can’t 
Although Mori shows folder and file icons for convenience and orientation, all the nodes of its hierarchy are essentially similar. An “entry” (node) can contain a styled text document (rtfd, displayed in a TextEdit-style pane), user-defined metadata (displayed in columns) and other entries as subentries. Entries that contain other entries are represented as folders; those that do not are represented as files. This means that folders can and often do directly incorporate user notes related to their contents–an excellent feature for annotating collections of documents. It also means that you can convert a file to a folder with a simple menu choice (which basically just swaps the icon representing the entry). This design is very flexible and, it turns out, quite powerful: users can decide whether they wish to annotate a collection of documents at the “containing folder” level, or create subentries to an entry containing a document–essentially as footnotes annotating that document.