If I do the following

php bin/magento maintenance:enable
composer require magento/product-community-edition 2.3.3 --no-update
composer update
rm -rf var/di var/generation
php bin/magento cache:flush
php bin/magento setup:upgrade
php bin/magento setup:di:compile
php bin/magento indexer:reindex
php bin/magento maintenance:disable

This all seems to work and the upgrade works as expected. The issue is though any files changed in the following DIRs do not get updated

  • /lib
  • /setup
  • /dev
  • / (the root)

What's the correct way of getting these files updated?

I know these are not being updated as if I create a brand new project and compare files in these folders I can see the files are different in the brand new project to the project I am upgrading

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