Regarding sorting notes into folders after the fact…
I use tags in my notes, so in that sense, the notes already have a virtual structure, I just need to find all the Concept notes tagged with #psychology say, and move them into a Psychology folder within the Concept folder.
My OS indexes file contents, so I just went to my OS Concepts folder, and searched for #psychology, and all the files(notes) that have the tag can now be moved into the new Psychology folder.
The problem with OS folders versus tags is that many notes have multiple tags and therefore, if I move it into one folder, its can’t be in another folder. Making duplicate notes or mirrored notes is silly.
What we need is for Obsidian to institute Virtual Folders, which are just tags, then a note could be in many “folders” at once. The left navigation pane in Obsidian could have an OS Folders or Virtual Folders switch.
And if you think about it, this is just a permanent tag search pane at that point.
There may still be a need for OS Folders in the case I mentioned above, having a vault with 10000 notes in a single folder might not work, but inside Obsidian, it could have all the virtual structure you wanted.
People have proposed the virtual folder idea, but I don’t know if it made it onto the Obsidian timeline.
The alternative to all this, is creating MoCs with the “Text ({expand}}” plugin. This can easily create a note with a dynamic list of note links that satisfy a criteria, for example, contain a certain #tag. In that way, you are getting a Virtual Folder of sorts. People probably don’t realize that this is why MoCs are a big deal, they are virtual folders. Also, that plugin shows the links in Edit Mode as well as Preview Mode.