Please delete this directory manually (2 replies)

After the database upgrade to 2.0.2, a warning came up asking to delete some subfolders manually. In this particular case it was:

Warning messages:

Warnings during the update: <br>Please delete this directory manually (eg. using your FTP software): /.../plugins/Referers
<br>Please delete this directory manually (eg. using your FTP software): /.../plugins/PDFReports 

Warnings during the update: <br>Please delete this directory manually (eg. using your FTP software): /.../libs/Smarty 
<br>Please delete this directory manually (eg. using your FTP software): /.../libs/Event

I haven't found any reference to this on the piwik.org and that's why I'm posting about it.

Why would this happen?

Thanks