Versioning for template directory?

Hi,

as more and more hooks are added to git, I would want to have the hook 
scripts, part of the per-repository configuration, itself in version control. 
If you look at CVS, the configuration there is also under version control (in 
CVSROOT). I can do this manually: after git-init-db, go into .git/hooks, do a 
git-init-db again, adding the hooks for version control, and commiting the 
initial version of the hooks.

But I get the feeling that the different hooks should be versioned 
on a file basis, and not on a directory/whole project basis.
Here, I explicitly want to have the RCS/CVS way of versioning.
[Another use case: a wiki site managed via a GIT archive, to be able to change 
the site offline. Here too, I would want to have versioning on a file basis]

Is there a way to "extend" git to allow for this kind of versioning? This 
needs multiple simultaneous checkouts of heads representing independent 
project parts (i.e. single files). There would be a GIT index for every such 
independent project part; the problem being that the checkouts should be done 
into the same directory.

So what is the best way to accomplish this?
I have to use multiple index files (index1, index2, ...), allowing multiple 
independent branches could be checked out independently. Another extension 
would be kind of a "super-head" specifying multiple heads (SHAs) 
which are to be checked out simultaneously (via index1, index2...). It should 
be possible to create signed tags out of such super-heads.

Is this feasable?

Josef