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You're not doing anything wrong. The current scoop installation script only creates a persistent directory for msys2: home. All other files will be replaced after scoop update msys2. The newly installed msys2 will only have the basic runtime; any packages manually installed with pacman will be lost.

To resolve this issue, might need to add clang64, clangarm64, mingw32, mingw64, ucrt64, usr, etc to the list of persistent directories. I'm not sure if this change would have any drawbacks.

msys2 can update itself (for example, using pacman -Syu). If you have many packages installed with pacman and need to update msys2 frequently, I recommend using the official msys2 installer.

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@Juemuren
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@wyzzoo
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