That's not an easy question. I think you need to enforce some style guide, like Wikipedia does.
org-mode is a bit like C++ or LaTeX. I say this as a good thing. It has tons of features, but you need to choose what to use and what to keep out.
For me, something that works great is to keep all org files in the same folder, with a flat structure. That includes my task list and my calendar. I version control everything, except organizational things that change often instead of growing like articles. I also keep out of version control first quick drafts of any article.
org-mode is a bit like C++ or LaTeX. I say this as a good thing. It has tons of features, but you need to choose what to use and what to keep out.
For me, something that works great is to keep all org files in the same folder, with a flat structure. That includes my task list and my calendar. I version control everything, except organizational things that change often instead of growing like articles. I also keep out of version control first quick drafts of any article.