Fix up some fallout from "setup_git_directory()" cleanups

Fix up some fallout from "setup_git_directory()" cleanups

git-ls-files was broken by the setup_git_directory() calling changes,
because I had missed the fact that the "prefix" variable in that file was
static to the whole file, and unlike git-ls-tree (where I had fixed it
up), it ended up using two different variables with the same name
depending on what the scoping happened to be.

This fixes it up properly (by just removing the static variable, and
passing the automatic one around properly), and git-ls-files should work
again.

Signed-off-by: Linus Torvalds <torvalds@osdl.org>
Signed-off-by: Junio C Hamano <junkio@cox.net>