cocci & cache.h: apply a selection of "pending" index-compatibility

Apply a selection of rules in "index-compatibility.pending.cocci"
tree-wide, and in doing so migrate them to
"index-compatibility.cocci".

As in preceding commits the only manual changes here are the macro
removals in "cache.h", and the update to the '*.cocci" rules. The rest
of the C code changes are the result of applying those updated rules.

Move rules for some rarely used cache compatibility macros from
"index-compatibility.pending.cocci" to "index-compatibility.cocci" and
apply them.

Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
diff --git a/builtin/checkout.c b/builtin/checkout.c
index aa610b2..afbd717 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -160,7 +160,8 @@ static int update_some(const struct object_id *oid, struct strbuf *base,
 		}
 	}
 
-	add_cache_entry(ce, ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
+	add_index_entry(&the_index, ce,
+			ADD_CACHE_OK_TO_ADD | ADD_CACHE_OK_TO_REPLACE);
 	return 0;
 }
 
@@ -744,7 +745,7 @@ static int merge_working_tree(const struct checkout_opts *opts,
 	if (read_cache_preload(NULL) < 0)
 		return error(_("index file corrupt"));
 
-	resolve_undo_clear();
+	resolve_undo_clear_index(&the_index);
 	if (opts->new_orphan_branch && opts->orphan_from_empty_tree) {
 		if (new_branch_info->commit)
 			BUG("'switch --orphan' should never accept a commit as starting point");