Libify the index refresh logic

This cleans up and libifies the "git update-index --[really-]refresh"
functionality. This will be eventually required for eventually doing the
"commit" and "status" commands as built-ins.

It really just moves "refresh_index()" from update-index.c to
read-cache.c, but it also has to change the calling convention so that the
function uses a "unsigned int flags" argument instead of various static
flags variables for passing down the information about whether to be quiet
or not, and allow unmerged entries etc.

That actually cleans up update-index.c too, since it turns out that all
those flags were really specific to that one function of the index update,
so they shouldn't have had file-scope visibility even before.

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