I use a flat folder structure. All my markdown files are in a single folder. I use metadata sections in the header of each document to organize and configure i

I use a flat folder structure. All my markdown files are in a single folder. I use metadata sections in the header of each document to organize and configure it. The documents themselves are structured differently depending on their topic. My journal document is a long running single document with timestamps. Other documents are structured in paragraphs, others are simply bulleted lists. Of course, everything is linked by tags, which are the core organizational mechanism. I've found that rigid organizational structures don't lead to better outcomes. It's best to let the structure develop naturally through tagging.