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Then within Settings, there should be "advanced settings" or "more..."

Also within Settings, there should be a tab for "system" and "user".

Doesn't mean they can't be logically grouped and presented using different tabs or even links, such as "Global settings", "User settings", etc. They may have different contexts, but they all fall under the purpose/concept of "customization". Discoverable doesn't have to imply unorganized.

Put all of the settings in the same area, and then segregate them by type in that area. Like how Firefox broadly does it. Every setting should be accessible from one central hub, and you can also make it accessible somewhere else if convenient.

> That’s because some settings are commonly changed, whereas others rarely. Cramming every single thing that can be construed as a “setting” into a single page results in a mess.

^apple's iOS