Picard 1.x has plugins in the Picard install directory and plugins in a user specific directory.

Since the new plugin functionality cannot update or delete plugins in the Picard install sub-directory (because only the installer and not Picard has write access to that directory), it probably makes sense for the installer to move any non-internal plugins from that directory to the user directory at install time. (Which assumes that the same user is installing 2.0 as will run Picard and that only 1 user will run Picard - which will be the case for most PCs using Picard but undoubtedly not all).