To start with, your data has some degree of built-in structure, especially if you have imported files from the Finder.
But to get the most from DEVONthink, you need to add further structure, making links and connections between files and groups of files.
When DEVONthink talks about "groups," it means documents that are bunched together because they share some meaning or theme. You can create groups yourself, and simply drag documents into them. Groups can have sub-groups, and they appear in the DEVONthink GUI as folders, so it helps to think of them as DEVONthink's Finder alternative.
Throughout DEVONthink, in search results windows and document windows, you will see the Classify button. Click it when viewing or previewing a document, and a drawer opens, offering you likely groups to which your document belongs.
Note that DEVONthink has already picked these for you, and is making suggestions based on the existing groups' contents. A brightly colored line icon appears next to each group suggestion; the longer the line, the better suited the current document is to that group.
What's happening is DEVONthink is trying to help you. The job of classifying documents remains yours, but the software attempts to make it quicker and easier by spotting themes and commonalities between documents and anticipating how they might be grouped together.
To move a document to a group, choose one of the suggestions from the list in the drawer and click the Move button. The behavior is like that of the Finder; the document disappears from where it was (either in another group, or ungrouped) and shifts location to the new group.
Remember that all of this is happening within DEVONthink's database; your original files, the ones you imported in the first place, are not touched.
Of course, if you have a lot of data (and as we shall see in the conclusions later on, DEVONthink is the kind of tool that suits people with a lot of data), the thought of manually classifying thousands of documents might be a little off-putting.
So there's an Auto Group command under the Data menu, which does a surprisingly good job of collating a mess of disorganized files into some kind of order. It could save you hours of work.
Documents can belong to more than one group. Right- or
Control-click a document, and you'll see a "Replicate to..." option. This makes an identical copy of your document (not an alias) and puts it in the group of your choice. The replicant document mirrors the original, even if the original is changed, and vice versa. Replicants are synchronized copies of their originals.
Duplicates, however, behave differently. A duplicate document exists independently of the original; edits made to it will not be reflected back.
You can ungroup things, too. Ungrouped documents move up one level of the groups hierarchy, all the way up to the top if need be, and will stay there until you assign them to a group.
There's a subtle difference between "grouping" and "classifying" in DEVONthink. Grouping is the process of creating groups of documents; classifying is the task of assigning documents to existing groups. You are more likely to spend time grouping when you first start using DEVONthink, and classifying once you've been using it for some time.
Also, DEVONthink works better if documents and groups are kept separate. In other words, don't have documents sitting alongside groups within the hierarchy; instead, create a new sibling group and put the spare documents in there.