I would like to deploy a directory to multiple developers having different permissions. So this is one thing Git cannot do. What about creating two repositories in one direc
A less annoying approach than git-submodules (which are a pain to use) is gitslave Gitslave creates a group of related repositories—a superproject repository and a number of slave repositories—all of which are concurrently developed on and on which all git operations should normally operate; so when you branch, each repository in the project is branched in turn. Similarly when you commit, push, pull, merge, tag, checkout, status, log, etc; each git command will run on the superproject and all slave repositories in turn. This sort of activity may be very familiar to CVS and (to a lesser extent) Subversion users. Gitslave's design is for simplicity for normal git operations.
I'll also point you to etckeeper which does track permissions. It has its own peculiarities which may or may not make it usable for you.
Finally, I'll note you can have a custome post-checkout script which sets the appropriate permissions on the appropriate files/directories.