Hello,

Same here (updated from 3.0.0) :

The three files above are backups I have done :

File to delete: index.html.old
File to delete: config/config.ini.php.old.old
File to delete: config/global.ini.php.new

Those above are not :

File to delete: libs/bower_components/jquery/src/ajax.js
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File to delete: libs/bower_components/jquery/src/core/init.js
File to delete: libs/bower_components/jquery/src/core/parseHTML.js
File to delete: libs/bower_components/jquery/src/core/ready.js
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File to delete: libs/bower_components/jquery/src/effects/support.js
File to delete: libs/bower_components/jquery/src/effects/Tween.js
File to delete: libs/bower_components/jquery/src/event/alias.js
File to delete: libs/bower_components/jquery/src/event/support.js
File to delete: libs/bower_components/jquery/src/exports/amd.js
File to delete: libs/bower_components/jquery/src/exports/global.js
File to delete: libs/bower_components/jquery/src/manipulation/_evalUrl.js
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File to delete: vendor/doctrine/annotations/composer.json
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File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/AnnotationReader.php
File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/AnnotationRegistry.php
File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/CachedReader.php
File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/DocLexer.php
File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/DocParser.php
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File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/IndexedReader.php
File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/PhpParser.php
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File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/SimpleAnnotationReader.php
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File to delete: vendor/doctrine/annotations/lib/Doctrine/Common/Annotations/Annotation/Attribute.php
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File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/ClearableCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/CouchbaseCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/FileCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/FilesystemCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/FlushableCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/MemcacheCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/MemcachedCache.php
File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/MongoDBCache.php
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File to delete: vendor/doctrine/cache/lib/Doctrine/Common/Cache/XcacheCache.php
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File to delete: vendor/doctrine/lexer/composer.json
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File to delete: vendor/doctrine/lexer/lib/Doctrine/Common/Lexer/AbstractLexer.php
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File to delete: vendor/monolog/monolog/src/Monolog/Handler/AmqpHandler.php
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File to delete: vendor/monolog/monolog/src/Monolog/Handler/ChromePHPHandler.php
File to delete: vendor/monolog/monolog/src/Monolog/Handler/CouchDBHandler.php
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File to delete: vendor/tecnickcom/tcpdf/fonts/kozminproregular.php
File to delete: vendor/tecnickcom/tcpdf/fonts/msungstdlight.php
File to delete: vendor/tecnickcom/tcpdf/fonts/stsongstdlight.php
File to delete: vendor/tecnickcom/tcpdf/fonts/symbol.php
File to delete: vendor/tecnickcom/tcpdf/fonts/zapfdingbats.php
File to delete: vendor/tecnickcom/tcpdf/include/sRGB.icc
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_colors.php
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_filters.php
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_font_data.php
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_fonts.php
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_images.php
File to delete: vendor/tecnickcom/tcpdf/include/tcpdf_static.php
File to delete: vendor/tecnickcom/tcpdf/include/barcodes/datamatrix.php
File to delete: vendor/tecnickcom/tcpdf/include/barcodes/pdf417.php
File to delete: vendor/tecnickcom/tcpdf/include/barcodes/qrcode.php
File to delete: vendor/tecnickcom/tcpdf/tools/convert_fonts_examples.txt
File to delete: vendor/tecnickcom/tcpdf/tools/tcpdf_addfont.php
File to delete: vendor/tedivm/jshrink/composer.json
File to delete: vendor/tedivm/jshrink/LICENSE
File to delete: vendor/tedivm/jshrink/package.xml
File to delete: vendor/tedivm/jshrink/phpunit.xml.dist
File to delete: vendor/tedivm/jshrink/README.md
File to delete: vendor/tedivm/jshrink/src/JShrink/Minifier.php
File to delete: vendor/twig/twig/CHANGELOG
File to delete: vendor/twig/twig/composer.json
File to delete: vendor/twig/twig/LICENSE
File to delete: vendor/twig/twig/phpunit.xml.dist
File to delete: vendor/twig/twig/README.rst
File to delete: vendor/twig/twig/ext/twig/config.m4
File to delete: vendor/twig/twig/ext/twig/config.w32
File to delete: vendor/twig/twig/ext/twig/php_twig.h
File to delete: vendor/twig/twig/ext/twig/twig.c
File to delete: vendor/twig/twig/lib/Twig/Autoloader.php
File to delete: vendor/twig/twig/lib/Twig/BaseNodeVisitor.php
File to delete: vendor/twig/twig/lib/Twig/CacheInterface.php
File to delete: vendor/twig/twig/lib/Twig/CompilerInterface.php
File to delete: vendor/twig/twig/lib/Twig/Compiler.php
File to delete: vendor/twig/twig/lib/Twig/Environment.php
File to delete: vendor/twig/twig/lib/Twig/Error.php
File to delete: vendor/twig/twig/lib/Twig/ExistsLoaderInterface.php
File to delete: vendor/twig/twig/lib/Twig/ExpressionParser.php
File to delete: vendor/twig/twig/lib/Twig/ExtensionInterface.php
File to delete: vendor/twig/twig/lib/Twig/Extension.php
File to delete: vendor/twig/twig/lib/Twig/FileExtensionEscapingStrategy.php
File to delete: vendor/twig/twig/lib/Twig/FilterCallableInterface.php
File to delete: vendor/twig/twig/lib/Twig/FilterInterface.php
File to delete: vendor/twig/twig/lib/Twig/Filter.php
File to delete: vendor/twig/twig/lib/Twig/FunctionCallableInterface.php
File to delete: vendor/twig/twig/lib/Twig/FunctionInterface.php
File to delete: vendor/twig/twig/lib/Twig/Function.php
File to delete: vendor/twig/twig/lib/Twig/LexerInterface.php
File to delete: vendor/twig/twig/lib/Twig/Lexer.php
File to delete: vendor/twig/twig/lib/Twig/LoaderInterface.php
File to delete: vendor/twig/twig/lib/Twig/Markup.php
File to delete: vendor/twig/twig/lib/Twig/NodeInterface.php
File to delete: vendor/twig/twig/lib/Twig/NodeOutputInterface.php
File to delete: vendor/twig/twig/lib/Twig/Node.php
File to delete: vendor/twig/twig/lib/Twig/NodeTraverser.php
File to delete: vendor/twig/twig/lib/Twig/NodeVisitorInterface.php
File to delete: vendor/twig/twig/lib/Twig/ParserInterface.php
File to delete: vendor/twig/twig/lib/Twig/Parser.php
File to delete: vendor/twig/twig/lib/Twig/SimpleFilter.php
File to delete: vendor/twig/twig/lib/Twig/SimpleFunction.php
File to delete: vendor/twig/twig/lib/Twig/SimpleTest.php
File to delete: vendor/twig/twig/lib/Twig/TemplateInterface.php
File to delete: vendor/twig/twig/lib/Twig/Template.php
File to delete: vendor/twig/twig/lib/Twig/TestCallableInterface.php
File to delete: vendor/twig/twig/lib/Twig/TestInterface.php
File to delete: vendor/twig/twig/lib/Twig/Test.php
File to delete: vendor/twig/twig/lib/Twig/TokenParserBrokerInterface.php
File to delete: vendor/twig/twig/lib/Twig/TokenParserBroker.php
File to delete: vendor/twig/twig/lib/Twig/TokenParserInterface.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser.php
File to delete: vendor/twig/twig/lib/Twig/Token.php
File to delete: vendor/twig/twig/lib/Twig/TokenStream.php
File to delete: vendor/twig/twig/lib/Twig/Cache/Filesystem.php
File to delete: vendor/twig/twig/lib/Twig/Cache/Null.php
File to delete: vendor/twig/twig/lib/Twig/Error/Loader.php
File to delete: vendor/twig/twig/lib/Twig/Error/Runtime.php
File to delete: vendor/twig/twig/lib/Twig/Error/Syntax.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Core.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Debug.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Escaper.php
File to delete: vendor/twig/twig/lib/Twig/Extension/GlobalsInterface.php
File to delete: vendor/twig/twig/lib/Twig/Extension/InitRuntimeInterface.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Optimizer.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Profiler.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Sandbox.php
File to delete: vendor/twig/twig/lib/Twig/Extension/Staging.php
File to delete: vendor/twig/twig/lib/Twig/Extension/StringLoader.php
File to delete: vendor/twig/twig/lib/Twig/Filter/Function.php
File to delete: vendor/twig/twig/lib/Twig/Filter/Method.php
File to delete: vendor/twig/twig/lib/Twig/Filter/Node.php
File to delete: vendor/twig/twig/lib/Twig/Function/Function.php
File to delete: vendor/twig/twig/lib/Twig/Function/Method.php
File to delete: vendor/twig/twig/lib/Twig/Function/Node.php
File to delete: vendor/twig/twig/lib/Twig/Loader/Array.php
File to delete: vendor/twig/twig/lib/Twig/Loader/Chain.php
File to delete: vendor/twig/twig/lib/Twig/Loader/Filesystem.php
File to delete: vendor/twig/twig/lib/Twig/Loader/String.php
File to delete: vendor/twig/twig/lib/Twig/Node/AutoEscape.php
File to delete: vendor/twig/twig/lib/Twig/Node/Block.php
File to delete: vendor/twig/twig/lib/Twig/Node/BlockReference.php
File to delete: vendor/twig/twig/lib/Twig/Node/Body.php
File to delete: vendor/twig/twig/lib/Twig/Node/CheckSecurity.php
File to delete: vendor/twig/twig/lib/Twig/Node/Do.php
File to delete: vendor/twig/twig/lib/Twig/Node/Embed.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression.php
File to delete: vendor/twig/twig/lib/Twig/Node/Flush.php
File to delete: vendor/twig/twig/lib/Twig/Node/ForLoop.php
File to delete: vendor/twig/twig/lib/Twig/Node/For.php
File to delete: vendor/twig/twig/lib/Twig/Node/If.php
File to delete: vendor/twig/twig/lib/Twig/Node/Import.php
File to delete: vendor/twig/twig/lib/Twig/Node/Include.php
File to delete: vendor/twig/twig/lib/Twig/Node/Macro.php
File to delete: vendor/twig/twig/lib/Twig/Node/Module.php
File to delete: vendor/twig/twig/lib/Twig/Node/Print.php
File to delete: vendor/twig/twig/lib/Twig/Node/SandboxedPrint.php
File to delete: vendor/twig/twig/lib/Twig/Node/Sandbox.php
File to delete: vendor/twig/twig/lib/Twig/Node/Set.php
File to delete: vendor/twig/twig/lib/Twig/Node/SetTemp.php
File to delete: vendor/twig/twig/lib/Twig/Node/Spaceless.php
File to delete: vendor/twig/twig/lib/Twig/Node/Text.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Array.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/AssignName.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/BlockReference.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Call.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Conditional.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Constant.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/ExtensionReference.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Filter.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Function.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/GetAttr.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/MethodCall.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Name.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/NullCoalesce.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Parent.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/TempName.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Unary.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Add.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/And.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/BitwiseAnd.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/BitwiseOr.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/BitwiseXor.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Concat.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Div.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/EndsWith.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Equal.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/FloorDiv.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/GreaterEqual.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Greater.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/In.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/LessEqual.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Less.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Matches.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Mod.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Mul.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/NotEqual.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/NotIn.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Or.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Power.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Range.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/StartsWith.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Binary/Sub.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Filter/Default.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Constant.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Defined.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Divisibleby.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Even.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Null.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Odd.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Test/Sameas.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Unary/Neg.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Unary/Not.php
File to delete: vendor/twig/twig/lib/Twig/Node/Expression/Unary/Pos.php
File to delete: vendor/twig/twig/lib/Twig/NodeVisitor/Escaper.php
File to delete: vendor/twig/twig/lib/Twig/NodeVisitor/Optimizer.php
File to delete: vendor/twig/twig/lib/Twig/NodeVisitor/SafeAnalysis.php
File to delete: vendor/twig/twig/lib/Twig/NodeVisitor/Sandbox.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Profile.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Dumper/Blackfire.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Dumper/Html.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Dumper/Text.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Node/EnterProfile.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/Node/LeaveProfile.php
File to delete: vendor/twig/twig/lib/Twig/Profiler/NodeVisitor/Profiler.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityError.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityNotAllowedFilterError.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityNotAllowedFunctionError.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityNotAllowedTagError.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityPolicyInterface.php
File to delete: vendor/twig/twig/lib/Twig/Sandbox/SecurityPolicy.php
File to delete: vendor/twig/twig/lib/Twig/Test/Function.php
File to delete: vendor/twig/twig/lib/Twig/Test/IntegrationTestCase.php
File to delete: vendor/twig/twig/lib/Twig/Test/Method.php
File to delete: vendor/twig/twig/lib/Twig/Test/Node.php
File to delete: vendor/twig/twig/lib/Twig/Test/NodeTestCase.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/AutoEscape.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Block.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Do.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Embed.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Extends.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Filter.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Flush.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/For.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/From.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/If.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Import.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Include.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Macro.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Sandbox.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Set.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Spaceless.php
File to delete: vendor/twig/twig/lib/Twig/TokenParser/Use.php
File to delete: vendor/twig/twig/lib/Twig/Util/DeprecationCollector.php
File to delete: vendor/twig/twig/lib/Twig/Util/TemplateDirIterator.php
File to delete: vendor/php-di/php-di/.phpstorm.meta.php

As upgrades overwrite modified core files and delete backups :

Modified files were :

plugins/API/Menu.php
core/Segment.php
API/Menu.php

backups of those "native" files (stored in the same folders) were deleted too on PIWIK upgrade.

Reading this : https://forum.piwik.org/t/elegant-way-to-override-core-functions/17456

What's the best way to do this ?

• a plugin ?
• manually upgrade ?

Thanks,

Eric

Thanks for the report. This PR will fix some of these messages and make it easier: #11123

It'll be included in 3.0.1-b2. Can you test again in few minutes and report here if there's

Unfortunately it is not fixed. Actually, I got more messages:

`Directories were found in your Piwik but we didn't expect them.
--> Please delete these directories to prevent errors. <--

Directory to delete: libs/bower_components/jScrollPane/issues
Directory to delete: libs/bower_components/jScrollPane/themes
Directory to delete: libs/bower_components/jquery/src
Directory to delete: vendor/doctrine/annotations
Directory to delete: vendor/doctrine/lexer
Directory to delete: vendor/mnapoli
Directory to delete: vendor/tecnick.com

To delete all these directories at once, you can run this command:
rm -Rf /opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/issues /opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/themes /opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery/src /opt/webdata/piwik-test.theyosh.nl/vendor/doctrine/annotations /opt/webdata/piwik-test.theyosh.nl/vendor/doctrine/lexer /opt/webdata/piwik-test.theyosh.nl/vendor/mnapoli /opt/webdata/piwik-test.theyosh.nl/vendor/tecnick.com

Files were found in your Piwik but we didn't expect them.
--> Please delete these files to prevent errors. <--

File to delete: libs/bower_components/jquery/MIT-LICENSE.txt
File to delete: libs/bower_components/jquery-placeholder/demo.html
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/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/bower_components/jqueryui-touch-punch/README.md
File to delete: libs/bower_components/jScrollPane/ajax_content.html
File to delete: libs/bower_components/jScrollPane/ajax.html
File to delete: libs/bower_components/jScrollPane/anchors.html
File to delete: libs/bower_components/jScrollPane/api.html
File to delete: libs/bower_components/jScrollPane/arrow_hover.html
File to delete: libs/bower_components/jScrollPane/arrow_positions.html
File to delete: libs/bower_components/jScrollPane/arrows.html
File to delete: libs/bower_components/jScrollPane/auto_reinitialise.html
File to delete: libs/bower_components/jScrollPane/basic.html
File to delete: libs/bower_components/jScrollPane/caps.html
File to delete: libs/bower_components/jScrollPane/changelog.html
File to delete: libs/bower_components/jScrollPane/destroy.html
File to delete: libs/bower_components/jScrollPane/drag_size.html
File to delete: libs/bower_components/jScrollPane/dynamic_content.html
File to delete: libs/bower_components/jScrollPane/dynamic_height.html
File to delete: libs/bower_components/jScrollPane/dynamic_width.html
File to delete: libs/bower_components/jScrollPane/events.html
File to delete: libs/bower_components/jScrollPane/faqs.html
File to delete: libs/bower_components/jScrollPane/fixed_width.html
File to delete: libs/bower_components/jScrollPane/focus.html
File to delete: libs/bower_components/jScrollPane/fullpage_scroll.html
File to delete: libs/bower_components/jScrollPane/GPL-LICENSE.txt
File to delete: libs/bower_components/jScrollPane/iframe2.html
File to delete: libs/bower_components/jScrollPane/iframe_content1.html
File to delete: libs/bower_components/jScrollPane/iframe_content2.html
File to delete: libs/bower_components/jScrollPane/iframe_content3.html
File to delete: libs/bower_components/jScrollPane/iframe_content4.html
File to delete: libs/bower_components/jScrollPane/iframe.html
File to delete: libs/bower_components/jScrollPane/image2.html
File to delete: libs/bower_components/jScrollPane/image.html
File to delete: libs/bower_components/jScrollPane/index.html
File to delete: libs/bower_components/jScrollPane/invisibles.html
File to delete: libs/bower_components/jScrollPane/known_issues.html
File to delete: libs/bower_components/jScrollPane/less_basic.html
File to delete: libs/bower_components/jScrollPane/mwheel_intent.html
File to delete: libs/bower_components/jScrollPane/override_animate.html
File to delete: libs/bower_components/jScrollPane/runeimp2.html
File to delete: libs/bower_components/jScrollPane/runeimp.html
File to delete: libs/bower_components/jScrollPane/scroll_on_left.html
File to delete: libs/bower_components/jScrollPane/scroll_to_animate.html
File to delete: libs/bower_components/jScrollPane/scroll_to.html
File to delete: libs/bower_components/jScrollPane/settings.html
File to delete: libs/bower_components/jScrollPane/short.html
File to delete: libs/bower_components/jScrollPane/v1.html
File to delete: libs/PiwikTracker/composer.json
File to delete: libs/PiwikTracker/LICENSE
File to delete: libs/PiwikTracker/README.md
File to delete: misc/others/iframeWidget.htm
File to delete: misc/phpstorm-codestyles/Piwik_codestyle.xml
File to delete: misc/phpstorm-codestyles/README.md
File to delete: vendor/pear/pear-core-minimal/src/PEAR5.php
File to delete: vendor/pear/pear-core-minimal/src/PEAR/ErrorStack5.php
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/DefinitionDumperDispatcher.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/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/device-detector/phpunit.xml.dist
File to delete: vendor/piwik/device-detector/misc/readme-report.php
File to delete: vendor/piwik/device-detector/misc/test.php
File to delete: libs/bower_components/jquery-ui/ui/.jshintrc
File to delete: vendor/monolog/monolog/.php_cs
File to delete: vendor/pear/archive_tar/.travis.sh
File to delete: vendor/piwik/device-detector/.php_cs
File to delete: vendor/twig/twig/.editorconfig

To delete all these files at once, you can run this command:
rm "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery/MIT-LICENSE.txt" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery-placeholder/demo.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery-placeholder/LICENSE-MIT.txt" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery-placeholder/README.md" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jqueryui-touch-punch/bower.json" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.js" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jqueryui-touch-punch/jquery.ui.touch-punch.min.js" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jqueryui-touch-punch/README.md" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/ajax_content.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/ajax.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/anchors.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/api.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/arrow_hover.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/arrow_positions.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/arrows.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/auto_reinitialise.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/basic.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/caps.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/changelog.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/destroy.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/drag_size.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/dynamic_content.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/dynamic_height.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/dynamic_width.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/events.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/faqs.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/fixed_width.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/focus.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/fullpage_scroll.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/GPL-LICENSE.txt" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe2.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe_content1.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe_content2.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe_content3.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe_content4.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/iframe.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/image2.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/image.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/index.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/invisibles.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/known_issues.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/less_basic.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/mwheel_intent.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/override_animate.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/runeimp2.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/runeimp.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/scroll_on_left.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/scroll_to_animate.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/scroll_to.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/settings.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/short.html" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jScrollPane/v1.html" "/opt/webdata/piwik-test.theyosh.nl/libs/PiwikTracker/composer.json" "/opt/webdata/piwik-test.theyosh.nl/libs/PiwikTracker/LICENSE" "/opt/webdata/piwik-test.theyosh.nl/libs/PiwikTracker/README.md" "/opt/webdata/piwik-test.theyosh.nl/misc/others/iframeWidget.htm" "/opt/webdata/piwik-test.theyosh.nl/misc/phpstorm-codestyles/Piwik_codestyle.xml" "/opt/webdata/piwik-test.theyosh.nl/misc/phpstorm-codestyles/README.md" "/opt/webdata/piwik-test.theyosh.nl/vendor/pear/pear-core-minimal/src/PEAR5.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/pear/pear-core-minimal/src/PEAR/ErrorStack5.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/AbstractFunctionCallDefinition.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/AliasDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/ArrayDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/DecoratorDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumperDispatcher.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/DefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/EnvironmentVariableDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/FactoryDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/StringDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Dumper/ValueDefinitionDumper.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Resolver/AliasResolver.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Resolver/StringResolver.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Definition/Resolver/ValueResolver.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/php-di/php-di/src/DI/Reflection/CallableReflectionFactory.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/piwik/device-detector/phpunit.xml.dist" "/opt/webdata/piwik-test.theyosh.nl/vendor/piwik/device-detector/misc/readme-report.php" "/opt/webdata/piwik-test.theyosh.nl/vendor/piwik/device-detector/misc/test.php" "/opt/webdata/piwik-test.theyosh.nl/libs/bower_components/jquery-ui/ui/.jshintrc" "/opt/webdata/piwik-test.theyosh.nl/vendor/monolog/monolog/.php_cs" "/opt/webdata/piwik-test.theyosh.nl/vendor/pear/archive_tar/.travis.sh" "/opt/webdata/piwik-test.theyosh.nl/vendor/piwik/device-detector/.php_cs" "/opt/webdata/piwik-test.theyosh.nl/vendor/twig/twig/.editorconfig"
`

I guess that an upgrade should clean up, and that it is not a user action after an upgrade. Because people will forget this.

@theyosh This now looks correct, and you can proceed deleting these files. maybe we should delete them automatically when possible. I'm creating this issue to keep track of this idea: Automatically delete non-expected files from the filesystem #11132