I resist the assertion that the order on the table reflects the order in one’s head, but I see some truth in it.
If you don’t process a newly downloaded/generated file and attach it to the right place, then this approach will soon lead to filling this folder with similar files.
Define the location of each file promptly. I am not saying that every file needs its own folder. Who said that a folder is exactly what should accompany a file? From the point of view of its role, a file is either a functional unit of some service’s code or it is an attachment, or a database, or a data container.
- In the first case (code), it’s a component of a website, web application, or service – here, a file structure is inherently needed, and everything is clear with this. Especially if the code is stored centrally, such as in Git.
- If the file is essentially an attachment (to be passed on or downloaded by other people), it should be placed where it will be downloaded/viewed. Attachments are not placed in a Git structure; they are issued as artifacts on special platforms, such as a Maven repository or simply a website with an attachment attached to the page.
- Databases require a specific structure and you probably won’t make mistakes with this, otherwise the database will not work.
- Under a data container can be understood either a container architecture (Docker) for integration into working environments, or standalone units such as files with a movie. In the first case, the rules are strict, but it’s difficult to make a mistake there, and in the second – you manage the structure yourself.
As you’ve realized, the context is about planning the placement of a file based on its future use. If you don’t care about the prospect of using the file, then it means you don’t need it. No file needed - delete it. No file - no worries 
Recently we will discuss whether it’s correct to apply the approach “throw away unnecessary things from your home.” And here we have to remember that I am not entirely in agreement with the assertion “the order on the table reflects the order in one’s head.”
