Pls refer to:
https://forum.piwik.org/t/unerwartete-verzeichnisse-bitte-loschen/25982

After updating Piwik-3.1.1 >> 3.2.1 system integrity check shows several essential core directories and files as 'deletable'. Further investigation shows the imperative need of marked files for Piwik functionality, so they must not be deleted!
There must be something wrong with the integrity check and resulting recommendations.

Test system:
Windows 7prof (64)
XAMPP for Windows 5.6.21
Piwik-Version: 3.2.1
MySQL-Version: 5.5.5
PHP-Version: 5.6.21