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Move packages to non-protected folder
MikTek is installing everything in program files which requires admin permissions. This is not proper usage of the Windows folder hierarchy.
I suggest that only Miktex binaries stay in %ProgramFiles% and move everything that requires modifications(like packages) to %ProgramData% for shared installations, and use %AppData%/%LocalAppData% for user specific installations.
MiKTeX binaries are distributed as packages (*-bin-2.9, *-bin-x64-2.9). At the moment, we make no distinction between binary and non-binary packages, i.e., everything will be installed in the installation directory (%LOCALAPPDATA%\Programs\MiKTeX 2.9 for a recommended MiKTeX installation).
It would be possible to separate the binaries from the MiKTeX distribution. We have done this on Linux and macOS. But for Windows, this is not on the agenda.
Is there any chance you would consider doing this?
I realize it's probably a big job and would take some time, but as it is a lot of bugs/errors/mistakes are made because of this layout. It would streamline the different OS installs and also improve security in a shared installation.
I will definitely consider this approach provided the MiKTeX community supports it (e.g., by giving enough thumb ups).
My workaround is to install MiKTeX to C:\MiKTeX and a user-installation only. Mostly, students use their machine vor their own. Thus, keeping two package databases updates adds more mental load to them. (Long howto at https://latextemplates.github.io/scientific-thesis-template/#installation-hints-for-windows).