I'm not sure if we really intend to prompt or not, but every time a user installs/updates the SDK through Studio they will get an overwrite prompt about 3/4 in to the process because we overwrite existing modules with the same ones from the new SDK (in other words, it seems like modules aren't underneath the SDK version folder, but are shared).
The prompt itself makes it so you force user interaction to finish the install, but it also can scare the user into thinking we're blowing something away. Do we really want to prompt if the normal use case is that some files will get overwritten? Maybe the files getting overwritten don't really need to? (i.e. the modules have the exact same content, so we don't even need to copy them over - which maybe we can get by comparing an MD5 hash recursively and filtering out files that already exist in the destination?)