treewide: add direct includes currently only pulled in transitively

The next commit will remove a bunch of unnecessary includes, but to do
so, we need some of the lower level direct includes that files rely on
to be explicitly specified.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

commit-graph.c

@@ -1,5 +1,6 @@
 #include "git-compat-util.h"
 #include "config.h"
+#include "csum-file.h"
 #include "gettext.h"
 #include "hex.h"
 #include "lockfile.h"