It’s possible to have hundreds of files in the same directory, as well as a Hierarchy of directories.
Each file can also have its own inner organization, including lists of header and trailer values, or tabulated value arrays, or whatever other arrangement you can imagine. There’s no better organization than yours, because you know your simulation and your application, as well as its algorithm and required parameters. But if your application will be used more than once, you have to write all this down—both so you can remember it and so you can share it with other scientists if the need arises. To achieve this, you need a formalism to describe the Context you have in mind and a structure to help you organize your data.
~