Write helpful message to FailureMarker if script execution time was exceeded during stage life cycle

I need to review

I don't think we want to use Failure marker for this. The class doc states

* The failure marker is a file placed in the active directory while staged
 * code is copied back into it, and then removed afterwards. This allows us to
 * know if a commit operation failed midway through, which could leave the site
 * code base in an indeterminate state -- which, in the worst case scenario,
 * might render Drupal being unable to boot.

So this is for a very particular purpose, "commit operation failed midway through, which could leave the site
* code base in an indeterminate state". I created #3360548: Document what the existence of the PACKAGE_MANAGER_FAILURE.yml means to make this clearer

I don't we should reuse it for this. We stop all operations if this file exists. The purpose of this file is that you can't trust your site's code at that point.

Of the 5 places we use this only during Apply would it leave your site's code base in an indeterminate state. But since it added to the first line of \Drupal\package_manager\StageBase::apply for all we know the time out is from very badly written PreApplyEvent subscriber. In that case we should not write the marker file. In StageBase::apply if call $this->committer->commit($stage_dir, $active_dir, $paths_to_exclude, NULL, $timeout); and we never return we will have already written the marker file and it will not be delete if the execution does not return to StageBase::apply. In that case still think we want to totally replace the file though in logExecutionTimeFailure as this MR does because it currently doesn't mention anything about restoring your site from a backup like \Drupal\package_manager\StageBase::getFailureMarkerMessage().

I will make some more specific suggestions in the MR

@Wim Leers can you update the summary to state concisely what the problem is we are trying to address. The Problem/Motivation section currently just links to another issue comment and that issue comment then mentions the 1 above it and then links to yet issue

Postponing this because re #10 I don't have the whole context of the problem space we are trying to solve