Piwik 3.0.0 Update: PHP Warning for CustomPiwikJs Plugin

After upgrading to Piwik 3.0.0 I got a lot of these PHP Warnings for CustomPiwikJS-Plugin:

WARNING: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/TrackingCode/PluginTrackerFiles.php(65): Warning - Invalid argument supplied for foreach() - Piwik 3.0.0 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)

WARNING: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/TrackingCode/PluginTrackerFiles.php(55): Warning - Invalid argument supplied for foreach() - Piwik 3.0.0 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)

Please delete the plugins/CustomPiwikJs/ as it’s not compatible with Piwik 3

I did, but now I get the following message in the administration panel:

File integrity check failed and reported some errors. You should fix this issue and then refresh this page until it shows no error.

Errors below may be due to a partial or failed upload of Piwik files.
→ Try to reupload all the Piwik files in BINARY mode. ←

Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/API.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/Commands/UpdateTracker.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/config/config.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/CustomPiwikJs.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/Diagnostic/PiwikJsCheck.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/Exception/AccessDeniedException.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/File.php
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/cs.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/de.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/el.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/en.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/es.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/fr.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/it.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/ja.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/nb.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/ru.json
Missing file: /var/www/vhosts/mydomain.de/stats.mydomain.de/plugins/CustomPiwikJs/lang/sq.json