File integrity check recommends deletion of essential files

I recently upgraded Piwik to the latest version of Matomo. It was a pretty hefty upgrade.

Everything went incredibly smooth, however now it reports that I have extraneous files in the piwik directory that I should delete. If I remove all the files it recommends, Matomo breaks, citing it can’t find Menu.php for a handful of (core) plugins.

Why is Matomo suggesting that I delete seemingly essential files?

Directories were found in your Matomo but we didn’t expect them.
–> Please delete these directories to prevent errors. <–

Directory to delete: libs/bower_components/jquery/src
Directory to delete: libs/pChart
Directory to delete: plugins/CoreUpdater/Test
Directory to delete: plugins/DevicePlugins/images
Directory to delete: plugins/DevicesDetection/images
Directory to delete: plugins/Diagnostics/Test
Directory to delete: plugins/LanguagesManager/Test
Directory to delete: plugins/Referrers/images
Directory to delete: plugins/UserCountry/images
Directory to delete: vendor/doctrine/annotations
Directory to delete: vendor/doctrine/lexer
Directory to delete: vendor/mnapoli

To delete all these directories at once, you can run this command:
rm -Rf /var/www/html/piwik/libs/bower_components/jquery/src /var/www/html/piwik/libs/pChart /var/www/html/piwik/plugins/CoreUpdater/Test /var/www/html/piwik/plugins/DevicePlugins/images /var/www/html/piwik/plugins/DevicesDetection/images /var/www/html/piwik/plugins/Diagnostics/Test /var/www/html/piwik/plugins/LanguagesManager/Test /var/www/html/piwik/plugins/Referrers/images /var/www/html/piwik/plugins/UserCountry/images /var/www/html/piwik/vendor/doctrine/annotations /var/www/html/piwik/vendor/doctrine/lexer /var/www/html/piwik/vendor/mnapoli

Files were found in your Matomo but we didn’t expect them.
–> Please delete these files to prevent errors. <–

File to delete: core/Measurable/MeasurableSetting.php
File to delete: core/Measurable/MeasurableSettings.php
File to delete: core/Measurable/Settings/Storage.php
File to delete: core/Menu/MenuMain.php
File to delete: core/Menu/MenuReporting.php
File to delete: core/Menu/MenuUser.php
File to delete: core/Plugin/Settings.php
File to delete: core/Plugin/Widgets.php
File to delete: core/PluginDeactivatedException.php
File to delete: core/Settings/Manager.php
File to delete: core/Settings/Storage.php
File to delete: core/Settings/Storage/StaticStorage.php
File to delete: core/Settings/StorageInterface.php
File to delete: core/Settings/SystemSetting.php
File to delete: core/Settings/UserSetting.php
File to delete: core/Tracker/SettingsStorage.php
File to delete: core/Updates/2.15.0-b4.php
File to delete: core/Updates/2.16.1-b3.php
File to delete: core/Updates/2.3.0-rc2.php
File to delete: core/Updates/2.4.0-b2.php
File to delete: core/View/ReportsByDimension.php
File to delete: core/WidgetsList.php
File to delete: libs/bower_components/jquery-placeholder/LICENSE-MIT.txt
File to delete: libs/bower_components/jquery-placeholder/README.md
File to delete: libs/bower_components/jqueryui-touch-punch/README.md
File to delete: libs/bower_components/jqueryui-touch-punch/bower.json
File to delete: libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.js
File to delete: libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.min.js
File to delete: libs/jquery/MIT-LICENSE-smartbanner.txt
File to delete: libs/jquery/jquery.smartbanner.js
File to delete: libs/jquery/stylesheets/jquery.smartbanner.css
File to delete: libs/sparkline/lib/Object.php
File to delete: misc/How to install Piwik.html
File to delete: plugins/Actions/Controller.php
File to delete: plugins/Actions/Menu.php
File to delete: plugins/Actions/stylesheets/dataTableActions.less
File to delete: plugins/Actions/templates/indexSiteSearch.twig
File to delete: plugins/Contents/Controller.php
File to delete: plugins/Contents/Menu.php
File to delete: plugins/Contents/stylesheets/datatable.less
File to delete: plugins/CoreAdminHome/javascripts/generalSettings.js
File to delete: plugins/CoreAdminHome/javascripts/jsTrackingGenerator.js
File to delete: plugins/CoreAdminHome/javascripts/pluginSettings.js
File to delete: plugins/CoreAdminHome/templates/pluginSettings.twig
File to delete: plugins/CoreConsole/Commands/ManagePlugin.php
File to delete: plugins/CoreHome/Visitor.php
File to delete: plugins/CoreHome/Widgets.php
File to delete: plugins/CoreHome/images/bg_header.jpg
File to delete: plugins/CoreHome/images/bullet1.gif
File to delete: plugins/CoreHome/images/bullet2.gif
File to delete: plugins/CoreHome/images/googleplay.png
File to delete: plugins/CoreHome/images/more_date.gif
File to delete: plugins/CoreHome/images/more_period.gif
File to delete: plugins/CoreHome/javascripts/menu.js
File to delete: plugins/CoreHome/javascripts/menu_init.js
File to delete: plugins/CoreHome/templates/ReportsByDimension/_reportsByDimension.twig
File to delete: plugins/CorePluginsAdmin/Marketplace.php
File to delete: plugins/CorePluginsAdmin/MarketplaceApiClient.php
File to delete: plugins/CorePluginsAdmin/MarketplaceApiException.php
File to delete: plugins/CorePluginsAdmin/Tasks.php
File to delete: plugins/CorePluginsAdmin/UpdateCommunication.php
File to delete: plugins/CorePluginsAdmin/images/paypal_donate.jpg
File to delete: plugins/CorePluginsAdmin/images/rating_important.png
File to delete: plugins/CorePluginsAdmin/javascripts/marketplace.js
File to delete: plugins/CorePluginsAdmin/javascripts/pluginExtend.js
File to delete: plugins/CorePluginsAdmin/javascripts/pluginOverview.js
File to delete: plugins/CorePluginsAdmin/javascripts/plugins.js
File to delete: plugins/CorePluginsAdmin/lang/hr.json
File to delete: plugins/CorePluginsAdmin/stylesheets/marketplace.less
File to delete: plugins/CorePluginsAdmin/stylesheets/plugin-details.less
File to delete: plugins/CorePluginsAdmin/templates/installPlugin.twig
File to delete: plugins/CorePluginsAdmin/templates/marketplace.twig
File to delete: plugins/CorePluginsAdmin/templates/marketplace/plugin-list.twig
File to delete: plugins/CorePluginsAdmin/templates/pluginDetails.twig
File to delete: plugins/CorePluginsAdmin/templates/updatePlugin.twig
File to delete: plugins/DBStats/stylesheets/dbStatsTable.less
File to delete: plugins/DevicePlugins/Visitor.php
File to delete: plugins/DevicesDetection/Segment.php
File to delete: plugins/DevicesDetection/Visitor.php
File to delete: plugins/DevicesDetection/templates/devices.twig
File to delete: plugins/DevicesDetection/templates/software.twig
File to delete: plugins/Ecommerce/Menu.php
File to delete: plugins/Ecommerce/Widgets.php
File to delete: plugins/Ecommerce/templates/ecommerceLog.twig
File to delete: plugins/Events/Controller.php
File to delete: plugins/Events/Menu.php
File to delete: plugins/Events/Segment.php
File to delete: plugins/Events/templates/index.twig
File to delete: plugins/ExamplePlugin/Widgets.php
File to delete: plugins/ExampleSettingsPlugin/Settings.php
File to delete: plugins/Goals/Widgets.php
File to delete: plugins/Goals/javascripts/goalsForm.js
File to delete: plugins/Goals/templates/_titleAndEvolutionGraph.twig
File to delete: plugins/Goals/templates/getGoalReportView.twig
File to delete: plugins/Goals/templates/getOverviewView.twig
File to delete: plugins/Insights/Widgets.php
File to delete: plugins/Live/Widgets.php
File to delete: plugins/Live/images/avatar_frame.png
File to delete: plugins/Live/images/paperclip.png
File to delete: plugins/Live/images/pause.gif
File to delete: plugins/Live/images/play.gif
File to delete: plugins/Live/images/returningVisitor.gif
File to delete: plugins/Live/images/unknown_avatar.jpg
File to delete: plugins/Live/images/visitor_profile_background.jpg
File to delete: plugins/Live/images/visitor_profile_close.png
File to delete: plugins/Live/images/visitor_profile_gradient.png
File to delete: plugins/Live/templates/getSingleVisitSummary.twig
File to delete: plugins/MobileAppMeasurable/config/test.php
File to delete: plugins/MobileMessaging/javascripts/MobileMessagingSettings.js
File to delete: plugins/MobileMessaging/templates/userSettings.twig
File to delete: plugins/Morpheus/fonts/piwik.eot
File to delete: plugins/Morpheus/images/calendar.gif
File to delete: plugins/Morpheus/images/collapsed_arrows.gif
File to delete: plugins/Morpheus/images/ecommerceAbandonedCart.gif
File to delete: plugins/Morpheus/images/ecommerceOrder.gif
File to delete: plugins/Morpheus/images/expanded_arrows.gif
File to delete: plugins/Morpheus/images/icon-calendar.gif
File to delete: plugins/Morpheus/images/li_dbl_gray.gif
File to delete: plugins/Morpheus/images/link.gif
File to delete: plugins/Morpheus/images/paypal_subscribe.gif
File to delete: plugins/Morpheus/javascripts/jquery.icheck.min.js
File to delete: plugins/Morpheus/javascripts/morpheus.js
File to delete: plugins/Morpheus/stylesheets/ieonly.css
File to delete: plugins/Morpheus/stylesheets/ui/_alerts.less
File to delete: plugins/Morpheus/templates/javascriptCode.tpl
File to delete: plugins/Morpheus/templates/settingsMacros.twig
File to delete: plugins/Morpheus/templates/user.twig
File to delete: plugins/MultiSites/images/arrow_asc.gif
File to delete: plugins/MultiSites/images/arrow_desc.gif
File to delete: plugins/PrivacyManager/javascripts/privacySettings.js
File to delete: plugins/ProfessionalServices/Widgets.php
File to delete: plugins/Provider/Visitor.php
File to delete: plugins/Referrers/Menu.php
File to delete: plugins/Referrers/Segment.php
File to delete: plugins/Referrers/Visitor.php
File to delete: plugins/Referrers/Widgets.php
File to delete: plugins/Referrers/templates/allReferrers.twig
File to delete: plugins/Referrers/templates/getSearchEnginesAndKeywords.twig
File to delete: plugins/Referrers/templates/index.twig
File to delete: plugins/Referrers/templates/indexWebsites.twig
File to delete: plugins/Resolution/Segment.php
File to delete: plugins/Resolution/Visitor.php
File to delete: plugins/SEO/Metric/Dmoz.php
File to delete: plugins/SEO/Widgets.php
File to delete: plugins/SEO/images/majesticseo.png
File to delete: plugins/SEO/images/whois.png
File to delete: plugins/ScheduledReports/javascripts/pdf.js
File to delete: plugins/SitesManager/templates/dialogs/edit-dialog.html
File to delete: plugins/SitesManager/templates/measurable_type_settings.twig
File to delete: plugins/UserCountry/Segment.php
File to delete: plugins/UserCountry/Visitor.php
File to delete: plugins/UserCountry/javascripts/userCountry.js
File to delete: plugins/UserCountry/templates/getGeoIpUpdaterManageScreen.twig
File to delete: plugins/UserCountry/templates/index.twig
File to delete: plugins/UserCountryMap/Menu.php
File to delete: plugins/UserCountryMap/svg/SDS.svg
File to delete: plugins/UserCountryMap/svg/TIB.svg
File to delete: plugins/UserLanguage/Visitor.php
File to delete: plugins/UsersManager/javascripts/giveViewAccess.js
File to delete: plugins/UsersManager/javascripts/usersManager.js
File to delete: plugins/UsersManager/javascripts/usersSettings.js
File to delete: plugins/VisitFrequency/Menu.php
File to delete: plugins/VisitFrequency/Widgets.php
File to delete: plugins/VisitFrequency/templates/_sparklines.twig
File to delete: plugins/VisitFrequency/templates/getSparklines.twig
File to delete: plugins/VisitFrequency/templates/index.twig
File to delete: plugins/VisitTime/Columns/ServerTime.php
File to delete: plugins/VisitTime/Controller.php
File to delete: plugins/VisitTime/Menu.php
File to delete: plugins/VisitTime/Segment.php
File to delete: plugins/VisitTime/templates/index.twig
File to delete: plugins/VisitorInterest/Controller.php
File to delete: plugins/VisitorInterest/Menu.php
File to delete: plugins/VisitorInterest/templates/index.twig
File to delete: plugins/VisitsSummary/Menu.php
File to delete: plugins/VisitsSummary/Widgets.php
File to delete: plugins/Widgetize/javascripts/widgetize.js
File to delete: vendor/monolog/monolog/CHANGELOG.mdown
File to delete: vendor/monolog/monolog/README.mdown
File to delete: vendor/pear/pear-core-minimal/copy-from-pear-core.sh
File to delete: vendor/php-di/php-di/src/DI/Definition/AbstractFunctionCallDefinition.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/AliasDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/ArrayDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/DecoratorDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumperDispatcher.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/EnvironmentVariableDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/FactoryDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/StringDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Dumper/ValueDefinitionDumper.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Resolver/AliasResolver.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Resolver/StringResolver.php
File to delete: vendor/php-di/php-di/src/DI/Definition/Resolver/ValueResolver.php
File to delete: vendor/php-di/php-di/src/DI/Reflection/CallableReflectionFactory.php
File to delete: vendor/piwik/referrer-spam-blacklist/CONTRIBUTING.md
File to delete: vendor/piwik/referrer-spam-blacklist/README.md
File to delete: vendor/piwik/referrer-spam-blacklist/composer.json
File to delete: vendor/piwik/referrer-spam-blacklist/spammers.txt
File to delete: vendor/piwik/searchengine-and-social-list/README.md
File to delete: vendor/piwik/searchengine-and-social-list/SearchEngines.yml
File to delete: vendor/piwik/searchengine-and-social-list/Socials.yml
File to delete: vendor/piwik/searchengine-and-social-list/composer.json
File to delete: vendor/tecnickcom/tcpdf/CHANGELOG.TXT

To delete all these files at once, you can run this command:
rm “/var/www/html/piwik/core/Measurable/MeasurableSetting.php” “/var/www/html/piwik/core/Measurable/MeasurableSettings.php” “/var/www/html/piwik/core/Measurable/Settings/Storage.php” “/var/www/html/piwik/core/Menu/MenuMain.php” “/var/www/html/piwik/core/Menu/MenuReporting.php” “/var/www/html/piwik/core/Menu/MenuUser.php” “/var/www/html/piwik/core/Plugin/Settings.php” “/var/www/html/piwik/core/Plugin/Widgets.php” “/var/www/html/piwik/core/PluginDeactivatedException.php” “/var/www/html/piwik/core/Settings/Manager.php” “/var/www/html/piwik/core/Settings/Storage.php” “/var/www/html/piwik/core/Settings/Storage/StaticStorage.php” “/var/www/html/piwik/core/Settings/StorageInterface.php” “/var/www/html/piwik/core/Settings/SystemSetting.php” “/var/www/html/piwik/core/Settings/UserSetting.php” “/var/www/html/piwik/core/Tracker/SettingsStorage.php” “/var/www/html/piwik/core/Updates/2.15.0-b4.php” “/var/www/html/piwik/core/Updates/2.16.1-b3.php” “/var/www/html/piwik/core/Updates/2.3.0-rc2.php” “/var/www/html/piwik/core/Updates/2.4.0-b2.php” “/var/www/html/piwik/core/View/ReportsByDimension.php” “/var/www/html/piwik/core/WidgetsList.php” “/var/www/html/piwik/libs/bower_components/jquery-placeholder/LICENSE-MIT.txt” “/var/www/html/piwik/libs/bower_components/jquery-placeholder/README.md” “/var/www/html/piwik/libs/bower_components/jqueryui-touch-punch/README.md” “/var/www/html/piwik/libs/bower_components/jqueryui-touch-punch/bower.json” “/var/www/html/piwik/libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.js” “/var/www/html/piwik/libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.min.js” “/var/www/html/piwik/libs/jquery/MIT-LICENSE-smartbanner.txt” “/var/www/html/piwik/libs/jquery/jquery.smartbanner.js” “/var/www/html/piwik/libs/jquery/stylesheets/jquery.smartbanner.css” “/var/www/html/piwik/libs/sparkline/lib/Object.php” “/var/www/html/piwik/misc/How to install Piwik.html” “/var/www/html/piwik/plugins/Actions/Controller.php” “/var/www/html/piwik/plugins/Actions/Menu.php” “/var/www/html/piwik/plugins/Actions/stylesheets/dataTableActions.less” “/var/www/html/piwik/plugins/Actions/templates/indexSiteSearch.twig” “/var/www/html/piwik/plugins/Contents/Controller.php” “/var/www/html/piwik/plugins/Contents/Menu.php” “/var/www/html/piwik/plugins/Contents/stylesheets/datatable.less” “/var/www/html/piwik/plugins/CoreAdminHome/javascripts/generalSettings.js” “/var/www/html/piwik/plugins/CoreAdminHome/javascripts/jsTrackingGenerator.js” “/var/www/html/piwik/plugins/CoreAdminHome/javascripts/pluginSettings.js” “/var/www/html/piwik/plugins/CoreAdminHome/templates/pluginSettings.twig” “/var/www/html/piwik/plugins/CoreConsole/Commands/ManagePlugin.php” “/var/www/html/piwik/plugins/CoreHome/Visitor.php” “/var/www/html/piwik/plugins/CoreHome/Widgets.php” “/var/www/html/piwik/plugins/CoreHome/images/bg_header.jpg” “/var/www/html/piwik/plugins/CoreHome/images/bullet1.gif” “/var/www/html/piwik/plugins/CoreHome/images/bullet2.gif”
rm “/var/www/html/piwik/plugins/CoreHome/images/googleplay.png” “/var/www/html/piwik/plugins/CoreHome/images/more_date.gif” “/var/www/html/piwik/plugins/CoreHome/images/more_period.gif” “/var/www/html/piwik/plugins/CoreHome/javascripts/menu.js” “/var/www/html/piwik/plugins/CoreHome/javascripts/menu_init.js” “/var/www/html/piwik/plugins/CoreHome/templates/ReportsByDimension/_reportsByDimension.twig” “/var/www/html/piwik/plugins/CorePluginsAdmin/Marketplace.php” “/var/www/html/piwik/plugins/CorePluginsAdmin/MarketplaceApiClient.php” “/var/www/html/piwik/plugins/CorePluginsAdmin/MarketplaceApiException.php” “/var/www/html/piwik/plugins/CorePluginsAdmin/Tasks.php” “/var/www/html/piwik/plugins/CorePluginsAdmin/UpdateCommunication.php” “/var/www/html/piwik/plugins/CorePluginsAdmin/images/paypal_donate.jpg” “/var/www/html/piwik/plugins/CorePluginsAdmin/images/rating_important.png” “/var/www/html/piwik/plugins/CorePluginsAdmin/javascripts/marketplace.js” “/var/www/html/piwik/plugins/CorePluginsAdmin/javascripts/pluginExtend.js” “/var/www/html/piwik/plugins/CorePluginsAdmin/javascripts/pluginOverview.js” “/var/www/html/piwik/plugins/CorePluginsAdmin/javascripts/plugins.js” “/var/www/html/piwik/plugins/CorePluginsAdmin/lang/hr.json” “/var/www/html/piwik/plugins/CorePluginsAdmin/stylesheets/marketplace.less” “/var/www/html/piwik/plugins/CorePluginsAdmin/stylesheets/plugin-details.less” “/var/www/html/piwik/plugins/CorePluginsAdmin/templates/installPlugin.twig” “/var/www/html/piwik/plugins/CorePluginsAdmin/templates/marketplace.twig” “/var/www/html/piwik/plugins/CorePluginsAdmin/templates/marketplace/plugin-list.twig” “/var/www/html/piwik/plugins/CorePluginsAdmin/templates/pluginDetails.twig” “/var/www/html/piwik/plugins/CorePluginsAdmin/templates/updatePlugin.twig” “/var/www/html/piwik/plugins/DBStats/stylesheets/dbStatsTable.less” “/var/www/html/piwik/plugins/DevicePlugins/Visitor.php” “/var/www/html/piwik/plugins/DevicesDetection/Segment.php” “/var/www/html/piwik/plugins/DevicesDetection/Visitor.php” “/var/www/html/piwik/plugins/DevicesDetection/templates/devices.twig” “/var/www/html/piwik/plugins/DevicesDetection/templates/software.twig” “/var/www/html/piwik/plugins/Ecommerce/Menu.php” “/var/www/html/piwik/plugins/Ecommerce/Widgets.php” “/var/www/html/piwik/plugins/Ecommerce/templates/ecommerceLog.twig” “/var/www/html/piwik/plugins/Events/Controller.php” “/var/www/html/piwik/plugins/Events/Menu.php” “/var/www/html/piwik/plugins/Events/Segment.php” “/var/www/html/piwik/plugins/Events/templates/index.twig” “/var/www/html/piwik/plugins/ExamplePlugin/Widgets.php” “/var/www/html/piwik/plugins/ExampleSettingsPlugin/Settings.php” “/var/www/html/piwik/plugins/Goals/Widgets.php” “/var/www/html/piwik/plugins/Goals/javascripts/goalsForm.js” “/var/www/html/piwik/plugins/Goals/templates/_titleAndEvolutionGraph.twig” “/var/www/html/piwik/plugins/Goals/templates/getGoalReportView.twig” “/var/www/html/piwik/plugins/Goals/templates/getOverviewView.twig” “/var/www/html/piwik/plugins/Insights/Widgets.php” “/var/www/html/piwik/plugins/Live/Widgets.php” “/var/www/html/piwik/plugins/Live/images/avatar_frame.png” “/var/www/html/piwik/plugins/Live/images/paperclip.png” “/var/www/html/piwik/plugins/Live/images/pause.gif”
rm “/var/www/html/piwik/plugins/Live/images/play.gif” “/var/www/html/piwik/plugins/Live/images/returningVisitor.gif” “/var/www/html/piwik/plugins/Live/images/unknown_avatar.jpg” “/var/www/html/piwik/plugins/Live/images/visitor_profile_background.jpg” “/var/www/html/piwik/plugins/Live/images/visitor_profile_close.png” “/var/www/html/piwik/plugins/Live/images/visitor_profile_gradient.png” “/var/www/html/piwik/plugins/Live/templates/getSingleVisitSummary.twig” “/var/www/html/piwik/plugins/MobileAppMeasurable/config/test.php” “/var/www/html/piwik/plugins/MobileMessaging/javascripts/MobileMessagingSettings.js” “/var/www/html/piwik/plugins/MobileMessaging/templates/userSettings.twig” “/var/www/html/piwik/plugins/Morpheus/fonts/piwik.eot” “/var/www/html/piwik/plugins/Morpheus/images/calendar.gif” “/var/www/html/piwik/plugins/Morpheus/images/collapsed_arrows.gif” “/var/www/html/piwik/plugins/Morpheus/images/ecommerceAbandonedCart.gif” “/var/www/html/piwik/plugins/Morpheus/images/ecommerceOrder.gif” “/var/www/html/piwik/plugins/Morpheus/images/expanded_arrows.gif” “/var/www/html/piwik/plugins/Morpheus/images/icon-calendar.gif” “/var/www/html/piwik/plugins/Morpheus/images/li_dbl_gray.gif” “/var/www/html/piwik/plugins/Morpheus/images/link.gif” “/var/www/html/piwik/plugins/Morpheus/images/paypal_subscribe.gif” “/var/www/html/piwik/plugins/Morpheus/javascripts/jquery.icheck.min.js” “/var/www/html/piwik/plugins/Morpheus/javascripts/morpheus.js” “/var/www/html/piwik/plugins/Morpheus/stylesheets/ieonly.css” “/var/www/html/piwik/plugins/Morpheus/stylesheets/ui/_alerts.less” “/var/www/html/piwik/plugins/Morpheus/templates/javascriptCode.tpl” “/var/www/html/piwik/plugins/Morpheus/templates/settingsMacros.twig” “/var/www/html/piwik/plugins/Morpheus/templates/user.twig” “/var/www/html/piwik/plugins/MultiSites/images/arrow_asc.gif” “/var/www/html/piwik/plugins/MultiSites/images/arrow_desc.gif” “/var/www/html/piwik/plugins/PrivacyManager/javascripts/privacySettings.js” “/var/www/html/piwik/plugins/ProfessionalServices/Widgets.php” “/var/www/html/piwik/plugins/Provider/Visitor.php” “/var/www/html/piwik/plugins/Referrers/Menu.php” “/var/www/html/piwik/plugins/Referrers/Segment.php” “/var/www/html/piwik/plugins/Referrers/Visitor.php” “/var/www/html/piwik/plugins/Referrers/Widgets.php” “/var/www/html/piwik/plugins/Referrers/templates/allReferrers.twig” “/var/www/html/piwik/plugins/Referrers/templates/getSearchEnginesAndKeywords.twig” “/var/www/html/piwik/plugins/Referrers/templates/index.twig” “/var/www/html/piwik/plugins/Referrers/templates/indexWebsites.twig” “/var/www/html/piwik/plugins/Resolution/Segment.php” “/var/www/html/piwik/plugins/Resolution/Visitor.php” “/var/www/html/piwik/plugins/SEO/Metric/Dmoz.php” “/var/www/html/piwik/plugins/SEO/Widgets.php” “/var/www/html/piwik/plugins/SEO/images/majesticseo.png” “/var/www/html/piwik/plugins/SEO/images/whois.png” “/var/www/html/piwik/plugins/ScheduledReports/javascripts/pdf.js” “/var/www/html/piwik/plugins/SitesManager/templates/dialogs/edit-dialog.html” “/var/www/html/piwik/plugins/SitesManager/templates/measurable_type_settings.twig” “/var/www/html/piwik/plugins/UserCountry/Segment.php”
rm “/var/www/html/piwik/plugins/UserCountry/Visitor.php” “/var/www/html/piwik/plugins/UserCountry/javascripts/userCountry.js” “/var/www/html/piwik/plugins/UserCountry/templates/getGeoIpUpdaterManageScreen.twig” “/var/www/html/piwik/plugins/UserCountry/templates/index.twig” “/var/www/html/piwik/plugins/UserCountryMap/Menu.php” “/var/www/html/piwik/plugins/UserCountryMap/svg/SDS.svg” “/var/www/html/piwik/plugins/UserCountryMap/svg/TIB.svg” “/var/www/html/piwik/plugins/UserLanguage/Visitor.php” “/var/www/html/piwik/plugins/UsersManager/javascripts/giveViewAccess.js” “/var/www/html/piwik/plugins/UsersManager/javascripts/usersManager.js” “/var/www/html/piwik/plugins/UsersManager/javascripts/usersSettings.js” “/var/www/html/piwik/plugins/VisitFrequency/Menu.php” “/var/www/html/piwik/plugins/VisitFrequency/Widgets.php” “/var/www/html/piwik/plugins/VisitFrequency/templates/_sparklines.twig” “/var/www/html/piwik/plugins/VisitFrequency/templates/getSparklines.twig” “/var/www/html/piwik/plugins/VisitFrequency/templates/index.twig” “/var/www/html/piwik/plugins/VisitTime/Columns/ServerTime.php” “/var/www/html/piwik/plugins/VisitTime/Controller.php” “/var/www/html/piwik/plugins/VisitTime/Menu.php” “/var/www/html/piwik/plugins/VisitTime/Segment.php” “/var/www/html/piwik/plugins/VisitTime/templates/index.twig” “/var/www/html/piwik/plugins/VisitorInterest/Controller.php” “/var/www/html/piwik/plugins/VisitorInterest/Menu.php” “/var/www/html/piwik/plugins/VisitorInterest/templates/index.twig” “/var/www/html/piwik/plugins/VisitsSummary/Menu.php” “/var/www/html/piwik/plugins/VisitsSummary/Widgets.php” “/var/www/html/piwik/plugins/Widgetize/javascripts/widgetize.js” “/var/www/html/piwik/vendor/monolog/monolog/CHANGELOG.mdown” “/var/www/html/piwik/vendor/monolog/monolog/README.mdown” “/var/www/html/piwik/vendor/pear/pear-core-minimal/copy-from-pear-core.sh” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/AbstractFunctionCallDefinition.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/AliasDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/ArrayDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/DecoratorDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumperDispatcher.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/EnvironmentVariableDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/FactoryDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/StringDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Dumper/ValueDefinitionDumper.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Resolver/AliasResolver.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Resolver/StringResolver.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Definition/Resolver/ValueResolver.php” “/var/www/html/piwik/vendor/php-di/php-di/src/DI/Reflection/CallableReflectionFactory.php” “/var/www/html/piwik/vendor/piwik/referrer-spam-blacklist/CONTRIBUTING.md” “/var/www/html/piwik/vendor/piwik/referrer-spam-blacklist/README.md” “/var/www/html/piwik/vendor/piwik/referrer-spam-blacklist/composer.json” “/var/www/html/piwik/vendor/piwik/referrer-spam-blacklist/spammers.txt” “/var/www/html/piwik/vendor/piwik/searchengine-and-social-list/README.md” “/var/www/html/piwik/vendor/piwik/searchengine-and-social-list/SearchEngines.yml”
rm “/var/www/html/piwik/vendor/piwik/searchengine-and-social-list/Socials.yml” “/var/www/html/piwik/vendor/piwik/searchengine-and-social-list/composer.json” “/var/www/html/piwik/vendor/tecnickcom/tcpdf/CHANGELOG.TXT”

These are the files I had to restore to get it working again:

File to delete: plugins/Actions/Menu.php
File to delete: plugins/Contents/Menu.php
File to delete: plugins/Ecommerce/Menu.php
File to delete: plugins/Events/Menu.php
File to delete: plugins/Referrers/Menu.php
File to delete: plugins/UserCountryMap/Menu.php
File to delete: plugins/VisitFrequency/Menu.php
File to delete: plugins/VisitTime/Menu.php
File to delete: plugins/VisitorInterest/Menu.php
File to delete: plugins/VisitsSummary/Menu.php

You should first try a “clean” install.

  • Backup your config.ini.php
  • Delete everything in /var/www/html/piwik/
  • Download and extract https://builds.matomo.org/piwik.zip
  • Copy contents to /var/www/html/piwik/
  • Copy backed up config.ini.php to /var/www/html/piwik/config/
  • Reinstall all non core plugins that you need
  • Enjoy

I just checked some of them and they don’t exist in the latest Matomo version, so replacing everything as mentioned by @fdellwing is probably the best way to get a clean setup. (Maybe do it on a staging-server before trying out on the production-system)