When the VirtualStore feature is in effect, it is safe to let random users write into C:\ProgramData because other users won't see those files. This seemed to be the case when we introduced support for C:\ProgramData\Git\config. However, when that feature is not in effect (which seems to be the case in newer Windows 10 versions), we'd rather not use those files unless they come from a trusted source, such as an administrator. This change imitates the strategy chosen by PowerShell's native OpenSSH port to Windows regarding host key files: if a system file is owned neither by an administrator, a system account, or the current user, it is ignored.
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