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Unpopular opinion 

An application being powered by a single SQLite database file is better than being database-free.

The one .sqlite3 file is much easier to backup than a folder full of files.

For example, I prefer MediaWiki backed by a SQLite database over DokuWiki which stores articles directly in the file system.

Unpopular opinion 

@njoseph OTOH, if it's a bunch of files, you can keep it in version control easier.

Unpopular opinion 

@njoseph Use cases, though. If you want to do file sync with, say, syncthing or Nextcloud, a flat file/folder structure is highly preferable for a personal wiki. A sqlite file would practically rule it out because version conflicts would usually lead to data loss, much less likely in the filewise case.

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