[TASK] Move configuration code from bootstrap to ext:install

Some methods in boostrap silently change TYPO3_CONF_VARS to adapt
some settings. Those methods are moved to the install tool as
"silent upgrade" to write out configuration options.
The silent upgrade code within StepController is extracted to
an own class for better encapsulation.

Change-Id: Id68bfdce7ffb661fb341e21eb8a26a03fe76ac07
Resolves: #52287
Releases: 6.2
Reviewed-on: https://review.typo3.org/24060
Reviewed-by: Thomas Maroschik
Reviewed-by: Wouter Wolters
Reviewed-by: Markus Klein
Tested-by: Markus Klein
Reviewed-by: Christian Kuhn
Tested-by: Christian Kuhn