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Oh noes. :)
You're right that you can't "move" a document from one collection to another, but that's just because you may want to have a document in three or even more collections -- how would you go about moving it from one to another without touching its appearance in the remaining collections?
Also, you don't need to duplicate a document unless you want what you call an "independent" copy. There# sno such thing as "replicate" in Ulysses, because you can always have one document in multiple collectiopns -- and having multiple replicas of one document side-by-side doesn't make much sense, does it?
However, here's how you do it: Drag'n'drop a document onto the desired collection. This will ALWAYS leave the document in all other collections (and filters, for that matter). Then just drag'n'drop the dpocument out of the browser. This will remove the document from the collection.
So, to reiterate: dragging, dropping, moving out -- virtual operations, organizational.
Duplicating, deleting -- real operations, on the files.
Replicates: Ulysses uses collections and filters as virtual places. The files are not actually moved to these places. If you delete one collection, the documents in that collection are still there. If you have a collection named "chapter 1" and another named "send to printer" and a third named "delete asap", you can completely ignore each collection as far as document management goes. All documents always reside on the top-level (so to speak), and all you do with collections is creating shortcuts to single groups of documents (again, so to speak).
This is a different approach then DT takes, and it may not work well for some, especially if they expect Ulysses' behavior to be different, or rather: similar to that of a specific (other) application; DT in your case.
I understand that the way we handle collections may not be of much use for folks just using collections as "single folders representing a hierarchical structure". However, once you go and create arbitrary collections, e.g. "later", "Eileen" and so on, you don't have to deal with explicitly creating "replicants" or even think about the differences between "replicants" and "duplicates" or "clones" or "mirrors" or whatever one might call them.
That's not to say that some people would love to have it work another way. :)
What I could think of, though, is to add a drag'n'drop modifier for documents. Like... Alt-Drag or such, which would then move a document from one collection to another. This would throw up new questions, of course: Do we move this out of ALL collections or just out of one? How do we handle drags from filters? And, most importantly: Can we really introduce a "move" modifier which resembles the system-wide "copy"-modifier?
But we might very well consider this...
Duplicates: A contextual menu for duplicates was dropped from 2.0 due to time and some conceptual problems, but we're re-considerig it for 2.1. E.g., if you "duplicate" a document in one collection, you will expect it to show up in that collection, but not in all the others it may be in. You would also like to rename it, I guess, and you might want to move it to a different collection right away. We're not so sure how to deal with these expectations, seeing how the browser works differently altogether.
Regarding your drag'n'drop out of a collection problem: There should be a contextual menu item called "remove from collection". Does that show up? If not: Check if you're in "cumulated" mode (ctrl-click on the documents header). This mode will show each document only once, even if a document is in multiple collections AND you have multiple collections/filters selected. Problem in 2.0: If you have only one collection selected, it can't treat the view as "not cumulated". This is not a bug per se, but rather an oversight on our part, which we might try and fix in 2.1.
About cumulated/cumulative (?) view: You can select multiple collections in the browser. So you may select 10 collections and 20 filters all at once. Ulysses will display all of the documents in the documents browser, and you can chose if it shows these documents within the "boundaries" of the collections/filters, or as a flat list. We call this flat list "cumulated", but maybe "pooled" is better, dunno.
However, what it does is it will show every document only once, even if this document is part of multiple collections or show up in multiple filters. As a matter of fact, cumulated view is very useful if you're using filters a lot, and maybe not so much if you're only working with collections.
Duplicates: Yeah, it should replicate the menubar behavior, though this very behavior is not without problems. ;)
Thanks for your time, btw.