ProjectExplorer: Don't auto-remove manually added run configurations

This is a follow-up from QTCREATORBUG-28273, to make realize the original feature request and make the behaviour less unexpected in the case where the option "Create suitable run configurations automatically" is disabled (while the resolution of  QTCREATORBUG-28273 in particular improved the behaviour with that option enabled).

The suggested change is: If "Create suitable run configurations automatically" is disabled, don't remove run configurations, even if the corresponding target is (currently) missing.

This prevents run configurations that were likely added manually from being removed automatically. This can be relevant in projects with cmake arguments that control the targets created in the current build. Or when switching between branches with different sets of targets.

One reason to disable "Create suitable run configurations automatically" may be situations with a large number or targets, where the user is only interested in a small, manually curated subset. Automatically removing missing run configurations in this situation (which is the current behaviour without this patch), is confusing and unexpected.

This is related to the recent change 488624: "ProjectExplorer: Do not auto-remove customized run configurations", which ensures that run configurations which have modified settings are not removed automatically. This is great with "Create suitable run configurations automatically" enabled, since any missing run configurations would be added automatically, with their default settings, as soon as they re-appear as targets. However, if "Create suitable run configurations automatically" is not enabled, then in general all run-configurations are added manually, even those that are used with their default settings. They would have to be manually created over and over again, if the target frequently disappears and reappears (e.g. due to cmake setting changes or branch switches). In that case, it is reasonable to assume that most users don't expect / want their manually added configurations to be removed automatically.