koIDocument: mark getEffectivePrefsByName as deprecated.

It has no in-tree users, and its behaviour is basically magical.

(integrated from komodo (trunk) change 80924 by marky)

git-svn-id: https://svn.openkomodo.com/repos/openkomodo/trunk@13257 b87d16e7-d29f-4ee1-b5ec-817d645d335f