[!!!][TASK] Remove various deprecated arguments and methods

This change removes deprecated functionality:

- ReferenceIndex->updateIndex() is now either ProgressListenerInterface or null
- ExtensionManagementUtility->findService() expects an array as third argument
- BasicFileUtility->setFileExtensionPermissions() removed
- GeneralUtility->callUserFunction now expects object or null as third argument
- DataMapper->__construct does not expect $query to be set anymore
- ObjectAccess->setProperty - fourth argument removed

Resolves: #91613
Related: #91473
Releases: master
Change-Id: I39fa30f84201b0ed837f6ac0e6d27e1ddb15376d