I also got hit by this problem on Linux with Julia 1.8.5 (except that package update hangs at 100% rather than 99.9%…).
I’ve updated the thread with the solution (Pkg.update in Julia 1.5 uses github - #5 by pierre-haessig) because removing and adding back the General registry didn’t make a change (unless I missed something): the URL of my General is still https://github.com/JuliaRegistries/General.git.
I’ve the same output for readdir(joinpath(DEPOT_PATH[1], "registries")) as you: there are two “General…” files in that folder. Version info is 1.8.5 (the standard Linux binary freshly updated from Download Julia).
As for the environment variable, it seems unset:
julia> ENV["JULIA_PKG_SERVER"]
ERROR: KeyError: key "JULIA_PKG_SERVER" not found
Now, I don’t know how the package manager handles caches of a registry and perhaps not many changes occurred since yesterday, but today when running package update, I get a near instantaneous response:
pkg> update
Updating registry at `~/.julia/registries/General.toml`
No Changes to `~/.julia/environments/v1.8/Project.toml`
No Changes to `~/.julia/environments/v1.8/Manifest.toml`
And indeed it would be worth putting this in another thread, but I think only moderators can split threads (Edit: I’ve add the “off-topic” private flag on my first post above).