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MelonLoader has added support for recursive loading. This means mods, plugins and userLibs can all be placed in the same folder inside the profile folder instead of needing to copy each type to a specific subfolder. This in turn means we can namespace each installed mod into its own subfolder, which makes uninstalling the mods straightforward and removes the need to track installation state on a separate file.
The mod author still need to place plugins and userLibs to specific folders in their Thunderstore packages though.
In the profile, package's UserData folder (if any) gets copied to profile/UserData/[packageName] and everything else gets copied to profile/Mods/[packageName]. MelonLoader handles the rest.
This will require MelonLoader v0.6.7 or newer to work.