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A flat file system is a system in which every file in an operating system is at the same directory level. These primitive file systems were mostly used in early computing systems prior to the development of the hierarchical file systems that are used today.
Having every file in the same folder or at the same level of directory storage is a fairly simple design with some specific limitations. For instance, because every file is at the same directory level, each file needs its own unique name. It is also harder to isolate sets of files for specific purposes.
By contrast, hierarchical directories present a lot more versatility and sophistication. Even in earlier systems, the use of PC-DOS commands allowed users to search through multiple directory levels and store files accordingly. With the hierarchical file system, different files can have redundant names because they are stored in different folders. As hardware and software systems developed, hierarchical file systems, which became the norm, have increasingly been split up into various virtual hard drives for an even more complicated storage system, and flat file systems have largely become obsolete.