How to fix «Overriding view file `app/design/frontend/<package>/<theme>/Magento_Checkout/layout/override/theme/Magento/blank/checkout_index_index.xml` does not match to any of the files»?

#0 vendor\magento\framework\View\File\FileList.php(80): Magento\Framework\View\File\FileList\Collator->collate(Array, Array)
#1 vendor\magento\framework\View\Layout\File\Collector\Aggregated.php(93): Magento\Framework\View\File\FileList->replace(Array)
#2 var\generation\Magento\Framework\View\Layout\File\Collector\Aggregated\Proxy.php(95): Magento\Framework\View\Layout\File\Collector\Aggregated->getFiles(Object(Magento\Theme\Model\Theme\Interceptor), '*.xml')
#3 vendor\magento\framework\View\Model\Layout\Merge.php(685): Magento\Framework\View\Layout\File\Collector\Aggregated\Proxy->getFiles(Object(Magento\Theme\Model\Theme\Interceptor), '*.xml')
#4 vendor\magento\framework\View\Model\Layout\Merge.php(633): Magento\Framework\View\Model\Layout\Merge->_loadFileLayoutUpdatesXml()
#5 var\generation\Magento\Framework\View\Model\Layout\Merge\Interceptor.php(232): Magento\Framework\View\Model\Layout\Merge->getFileLayoutUpdatesXml()
#6 vendor\magento\framework\View\Model\Layout\Merge.php(527): Magento\Framework\View\Model\Layout\Merge\Interceptor->getFileLayoutUpdatesXml()
#7 vendor\magento\framework\View\Model\Layout\Merge.php(506): Magento\Framework\View\Model\Layout\Merge->_fetchPackageLayoutUpdates('default')
#8 vendor\magento\framework\View\Model\Layout\Merge.php(434): Magento\Framework\View\Model\Layout\Merge->_merge('default')
#9 var\generation\Magento\Framework\View\Model\Layout\Merge\Interceptor.php(193): Magento\Framework\View\Model\Layout\Merge->load(Array)
#10 vendor\magento\framework\View\Layout\Builder.php(86): Magento\Framework\View\Model\Layout\Merge\Interceptor->load()
#11 vendor\magento\framework\View\Layout\Builder.php(63): Magento\Framework\View\Layout\Builder->loadLayoutUpdates()
#12 vendor\magento\framework\View\Layout.php(244): Magento\Framework\View\Layout\Builder->build()
#13 vendor\magento\framework\View\Layout.php(859): Magento\Framework\View\Layout->build()

The exception is raised by the Magento\Framework\View\File\FileList\Collator::collate() method:

Magento 2.0.x contains the app/design/frontend/Magento/blank/Magento_Checkout/layout/checkout_index_index.xml layout.
Magento >= 2.1 does not contain this layout:
github.com/magento/magento2/tree/2.1.0/app/design/frontend/Magento/blank/Magento_Checkout.

So you need to mode the contents of your app/design/frontend/<package>/<theme>/Magento_Checkout/layout/override/theme/Magento/blank/checkout_index_index.xml file to the app/design/frontend/<package>/<theme>/Magento_Checkout/layout/checkout_index_index.xml file.