My ideas:
The important part is that the manifests block reasonable branching/merging 
cause it will allways cause collisions (yeah i know i can cherry pick). So 
possibility would be to remove the manifest from the first commit and commit 
them right afterwards. So the messages would look like:
* Fix gcc-4.3-issue for libfoo. Per bug #22222.
* Manifest for libfoo.
And for picking you would just pick the first ones and ignore manifest ones. 
The sidefect of this will be the spam on git log, where every second commit 
will be manifest. Any ideas/alternatives to this?
(this behavior really enables the picking as we want, alternative what i am 
right now able to think of is creating separate branch/server containing only 
manifests which would get merged for rsync... [which is of course insane 
overhead so dont even think about it :P])

Regards
Tomas Chvatal