Execute jobs on all index.php requests.

Execute jobs on all index.php requests.

The problem is that currently deferred updates are not executed
after action=ajax requests or file cache hits. This means that,
e.g. ViewCountUpdates are not executed after file cache hits.
The code to execute jobs (both deferred updates and job queue)
is now in MediaWiki::restInPeace() so that it's also executed
after what is mentioned above, and the remaining code of
MediaWiki::finalCleanup() is moved directly MediaWiki::main()
since that function is only used in one place and it make no
sense to keep a method for such little code.

Change-Id: I6f511a74c59a2e3653c10bfcff9b0d15118e699f