Fix behavior of Hooks class.

Fix behavior of Hooks class.

Until now, Hooks::run() would execute hooks registered via $wgHooks, but
Hooks:isRegistered() would not consider them and Hooks::getHandlers() would
not return them. That is inconsistent and misleading. This change aims to
make the methods of the Hooks class behave consistently, and allows them
to be used as a generic way of interacting with hooks.

Change-Id: I39bd5de2bc8ccbe8df729446363960af9d29b0be