Like @bogenschlag I have my stuff in ~/Documents, which is iCloud-synchronised.
So that’s currently three top-level folders:
- 101 Personal
- 102 Johnny.Decimal
- 104 Learn with Lucy
Then in each of those the usual 10-19 etc.
I also have a Synology which is currently hosting most of 104 Learn with Lucy, now that I think about it.
Some apps, especially those that cloud-sync, like to keep their own files in their own place. MindNode, for example. I generally just let them do this, using the file name to indicate where the thing ‘really’ belongs. I find this just works better.
If I stop editing a file and manage to remember to do so, I’ll then move it out of the shared cloud area and in to its ‘real’ home.