I beg to differ. Having them all in one folder is actually exactly what I want.
Storing them into folders is just giving you problems. I would need to put them into many folders, to get any benefits, but than again, this could be done by tags so much more easily.
In the end there is no reason to directly manipulate the file structure. It is just easier to have a flat hierarchy. If I need to find something: there are tags, there is the graph, and of course there is a full text search.
I partially agree with you, but it's because I have a certain searching method that I'm comfortable with. I use sed/awk/grep quite a bit. The find command is also useful - but with those utilities, I can quickly search for any string or regular expression I need.
If I'm looking for the word cow in a doc that I think is in a folder (even if it's in subfolders), then I can do this:
grep --color=always -r "cow"
(I like setting color to always, and for some reason I'm too lazy to set up an alias so I don't have to type it)
I can get way more complicated by escaping spaces, looking for certain file types, etc.... really this does about the same as grep though - but still interesting:
find -name ".txt" -o -name ".md" -type f | sed 's/\ /\\\ /'g | xargs grep --color=always -n "cow"
Using these utilities, I've been able to find things in lots of lines of code, or lots of lines of md files.
Well, I do have around 8000 documents, and I organize them with a mix of hierarchy and tags (plus search). My entire site (taoofmac.com) was built that way, but the hierarchy was key - otherwise I would have trouble grouping and managing related things.
Storing them into folders is just giving you problems. I would need to put them into many folders, to get any benefits, but than again, this could be done by tags so much more easily.
In the end there is no reason to directly manipulate the file structure. It is just easier to have a flat hierarchy. If I need to find something: there are tags, there is the graph, and of course there is a full text search.