Files as an interchange format, sure. But as a primary storage system for application structured data they leave a lot to be desired: - Portability of metadata

Files as an interchange format, sure. But as a primary storage system for application structured data they leave a lot to be desired: - Portability of metadata is lacking (and can be sneakily removed when you least expect it), as other commenters have pointed out. - Filtering sets of files from out of a (possibly deep) directory hierarchy based on different criteria requires writing a lot of subtly different loops to check metadata. Querying e.g. SQLite handles that part for you once you express what you want, without as much risk of messing up one of those loops. - Similarly, a schemaful database can prevent your writing incorrectly-shaped (meta)data up front, where filesystems are flexible enough that bad writes may not be noticed until your program tries to read that data back out. - The accessibility of file-based internal storage systems to human users can sometimes be too high, a la the joke about someone "organizing and renaming things in the win32 folder". Cracking open and messing about with a flat-file all-in-one DB is a higher barrier to screwing around. To be fair, permissions mitigate this risk substantially. - Intermediate failures with some single-flat-file DBs are much less impactful than with many filesystems. Two parts to this: one is that a more rigid structure in a DB prevents certain invalid writes entirely; the other is transactionality. While plenty of local-flat-file "myapp.library" DBs don't have a good atomicity story underneath (I'm always saddened when I poke at a proprietary data library format and find that it contains a bug-ridden, informally-specified implementation of half of SQLite), and while some file systems make logical atomicity possible to achieve (e.g. via CoW copying data/directories, doing mutations, atomically swapping a source-of-truth link to the new version, and dropping the old), filesystem-as-database systems tend to fail-corrupted often due to unexpected issues (from bugs to "oops, don't have write access on 1/1000 files" to SIGKILL/power loss/drive failure) during data modifications. While I wish more file-based systems were as robust as maildir, I won't hold my breath when SQLite is right there.