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The 2.8 manual states:

For locally extracted Blender distributions, the user configuration and run-time data are kept in the same subdirectory, allowing multiple Blender versions to run without conflict, ignoring the USER and SYSTEM files.

How exactly can I control this behaviour for "locally extracted" versions of blender?

Currently (2019-06-25) when I download the blender 2.8 development package and extract it on my harddisk, a change in the preferences will affect not only this specific version, but all parallel installations of blender. This behaviour is the same on windows and linux.

I'd like blender to ignore the USER and SYSTEM settings. How do I do this?

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Apparently there needs to be a "config" folder with the appropriate files inside the version folder of a locally extracted blender version (e.g. C:\BlenderTest\blender-2.80.0-git.c0c1b4542f39-windows64/2.80/) for it to ignore USER and SYSTEM settings.

Creating this folder and copying over the appropriate files "userpref.blend" and optionally "bookmarks.txt" and "recent-files.txt" isolates the respective blender.exe from the user and system settings. Any changes made from this executable are saved in the local userpref file.

See this answer for file paths under common operating systems.

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