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Sometimes a user's home directory may not be where you want to store regsistry keys for the current user (Registry.CurrentUser). Unfortunately, it looks as if mcs/class/corlib/Microsoft.Win32/UnixRegistryApi.cs:778 hardcodes this storage there. You can override the system storage directory at runtime using MONO_REGISTRY_PATH, but not the user one.
It would be better *anyway* if this used SpecialFolder.Config as that is the right place to put configuration files on *nix systems, but that would come with the added benefit of being able to be properly overridden at runtime (without resetting $HOME if my other patch gets accepted [currently you can't change it /at all/ because SpecialFolder.Personal is hardcoded]).
And/or another environment variable such as MONO_CURRENTUSER_REGISTRY_PATH could be used.
I have added a commit for this on https://github.com/adbre/mono/tree/iss358,
but I'm not so sure about the consequenses for this change, so I have not yet opened a pull request.
The discussion on github seems to be dead for a while, but the issue status is definitively not resolved yet. Since Adam wrote the man page and the fix is requested, maybe the bug should be reopened, and bumped?