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Ok, after some investigation, it turns out that the usage of Preferences.jl has following drawbacks:
It works only with Julia 1.6+. Of course, 1.6 is new LTS, so there is no need to support older versions. On the other hand, this is the only package, which adds this restriction, so it's a big impact with little value.
As it turns out, it is impossible to make Julia independent preferences, on the contrary, preferences are very fragmented. The only solution is to make changes to startup.jl, which kind of defeat the purpose. See: Another storing location JuliaPackaging/Preferences.jl#30 (comment)
So, Preferences.jl is useless in the context of the BenchmarkExt.jl project. It makes no sense to use it.
Currently I am using custom code to work with preferences. There is a project https://github.com/JuliaPackaging/Preferences.jl which should make it more reliable and stable.
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