Sorry for the slow answer. This is how I have my folders set up.
- Each project has its own folder, with a structure like this (I have many projects)
The exact structure depends on the project, of course. In the main folder I keep a single org-mode file for that project:
In that file I keep taks and TODOs (I include that file in my org-agenda-files). Until recently I kept the code for the analysis in that project as source code blocks in that file (I program in R). Now I switched to keep separate files with my scripts:
I use git to keep the files of each project under version control, and use projectile to quickly jump around files in each project.
I have a single folder with all my pdfs:
I also have a separate folder for my org-roam notes. I keep zettlekasten-type notes and literature notes in two separate subfolders:
In this way when I search for a note I can select in which kind of note to look.
Hopefully this will give you some ideas.