Introduce `bp_core_mark_notifications_by_type()` and `bp_core_mark_notifications_by_item_id()` and replace `bp_core_delete_notifications_by_type()` and `bp_core_delete_notifications_by_item_id()` usages.

Ensures notifications are toggled as acknowledged rather than deleted. See #5148.

git-svn-id: https://buddypress.svn.wordpress.org/trunk@7530 cdf35c40-ae34-48e0-9cc9-0c9da1808c22