[TASK] Remove empty array from site configuration before persisting

Having empty array like `routes: {  }` make it hard to lint the site
configuration yaml files. To have a cleaner state, those empty arrays
are removed before they are persisted.

Resolves: #92524
Releases: master, 10.4
Change-Id: Id4f9cae7deb5903bf735cc1076731a5105b494ec
Reviewed-on: https://review.typo3.org/c/Packages/TYPO3.CMS/+/66091


Tested-by: TYPO3com <noreply@typo3.com>
Tested-by: Benni Mack <benni@typo3.org>
Tested-by: Josef Glatz <josefglatz@gmail.com>
Tested-by: Markus Klein <markus.klein@typo3.org>
Tested-by: Oliver Bartsch <bo@cedev.de>
Tested-by: Georg Ringer <georg.ringer@gmail.com>
Reviewed-by: Benni Mack <benni@typo3.org>
Reviewed-by: Josef Glatz <josefglatz@gmail.com>
Reviewed-by: Markus Klein <markus.klein@typo3.org>
Reviewed-by: Oliver Bartsch <bo@cedev.de>
Reviewed-by: Georg Ringer <georg.ringer@gmail.com>