Update broken due to RemoveRootShares when an app needs update

[PVince81]

Steps

1. Setup OC with master (cc532bb)
2. Increase version in "version.php"
3. Run update on the CLI => works fine
4. Increase version of "files_sharing" in its info.xml (or any filesystem-related app)
5. Run update on the CLI => 💣

An unhandled exception has been thrown:
exception 'OC\NeedsUpdateException' in /srv/www/htdocs/owncloud/lib/private/legacy/app.php:147
Stack trace:
#0 /srv/www/htdocs/owncloud/lib/private/legacy/app.php(119): OC_App::loadApp('files_sharing')
#1 /srv/www/htdocs/owncloud/lib/private/legacy/util.php(135): OC_App::loadApps(Array)
#2 /srv/www/htdocs/owncloud/lib/private/Files/Filesystem.php(260): OC_Util::setupFS(NULL)
#3 /srv/www/htdocs/owncloud/lib/private/Server.php(174): OC\Files\Filesystem::getMountManager(NULL)
#4 /srv/www/htdocs/owncloud/3rdparty/pimple/pimple/src/Pimple/Container.php(113): OC\Server->OC\{closure}(Object(OC\Server))
#5 /srv/www/htdocs/owncloud/lib/private/AppFramework/Utility/SimpleContainer.php(102): Pimple\Container->offsetGet('RootFolder')
#6 /srv/www/htdocs/owncloud/lib/private/ServerContainer.php(87): OC\AppFramework\Utility\SimpleContainer->query('RootFolder')
#7 /srv/www/htdocs/owncloud/lib/private/Server.php(780): OC\ServerContainer->query('RootFolder')
#8 /srv/www/htdocs/owncloud/lib/private/Repair.php(140): OC\Server->getRootFolder()
#9 /srv/www/htdocs/owncloud/core/register_command.php(125): OC\Repair::getRepairSteps()
#10 /srv/www/htdocs/owncloud/lib/private/Console/Application.php(87): require_once('/srv/www/htdocs...')
#11 /srv/www/htdocs/owncloud/console.php(93): OC\Console\Application->loadCommands(Object(Symfony\Component\Console\Input\ArgvInput), Object(Symfony\Component\Console\Output\ConsoleOutput))
#12 /srv/www/htdocs/owncloud/occ(11): require_once('/srv/www/htdocs...')
#13 {main}

CC @rullzer

This is because the injection in the repair step happens too early.

Let's try calling getRootFolder only in the run phase.

[PVince81]

Fix is here #25158

[lock]

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