Replace 040000 and 0100644 constants with GIT_MODE_{TREE,FILE}

Replace 040000 and 0100644 constants with GIT_MODE_{TREE,FILE}

Those constants were scattered in *way* too many places.  While we're there,
fix the inconsistent usage of strings vs. ints when specifying the file
mode; there's no good reason to be passing strings around (except that I
foolishly did that in the original code in version 0.01).

Signed-off-by: Avery Pennarun <apenwarr@gmail.com>