Check and Remove ext_typoscript_setup.txt
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IMHO the file ext_typoscript_setup.txt can be removed safely.
The only setting, which is not default is config.tx_extbase.persistence.updateReferenceIndex = 0. But this shouldn't hurt.
What is/was the purpose of this file? It is not used anywhere in the source code. Is it some extension template leftover?
I noticed now the setting config.tx_extbase.persistence.updateReferenceIndex is false by default. So no setting in this file changes anything. We can delete it safely.
Internally, TYPO3 manages an index of all relationships between two datasets the so-called RefIndex. Due to this index it's possible to show the number of associated datasets in the list module's column [Ref.]. By clicking on the number you get further informations about the incoming and outgoing references of the dataset. This index is automatically updated when any datasets get edited. The configuration config.tx_extbase.persistence.updateReferenceIndex = 1 effects an update when datasets get edited in the Frontend though it is normally deactivated due to its huge effects on performance.
https://docs.typo3.org/typo3cms/ExtbaseFluidBook/6-Persistence/2-configure-the-backends-inputforms.html