refs #5936 remove gone files during update

As mentioned in the ticket when updating Piwik it will compare all directories within the plugins folder and the core directory of the latest.zip with the current installation and remove all files that are in the users current installation but not in the latest.zip.

To test it one has to update Piwik to make sure the CoreUpdater uses this new codebase and then update again to a later version. So it won't work directly with the next update. Maybe we can release to new betas and update after each?