I'd say it depends on what exactly you need to store. Database settings, base paths and cookie settings go into config files, and base urls, theme directories, images dirs, site name, etc. go into the database (in my apps). You can't just store EVERYTHING in the database. Depends on what level of flexibility you need on an application. I used for a long time .php config files (and settings inside it were stored as a big array), but I consider moving to .ini files.

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