Add an alter hook to EntityQuery

EntityFieldQuery in D7 had an alter hook. When we rewrote it for D8, we forgot to add an alter hook. The dead docs were removed in #2611638: hook_entity_query_alter() is dead, remove it from entity.api.php.

However, we definitely need it. It is currently a blocker for anyone looking to hardcode their own filtering behavior. Without hook_entity_query_alter() we need to alter the underlying SQL query, which is not trivial due to field storage (requires using Tables to add the joins, and copying the EntityQuery Condition logic for selecting a LEFT vs INNER join).

For examples of the difficulty in modifying entity queries using only the current hook_query_entity_reference() see block_content_query_entity_reference_alter() and the Query Access API (#777578: Add an entity query access API and deprecate hook_query_ENTITY_TYPE_access_alter()).

So, let's re-add the hook.