cocci: apply "pending" index-compatibility to some "builtin/*.c"

Apply "index-compatibility.pending.cocci" rule to "builtin/*", but
exclude those where we conflict with in-flight changes.

As a result some of them end up using only "the_index", so let's have
them use the more narrow "USE_THE_INDEX_VARIABLE" rather than
"USE_THE_INDEX_COMPATIBILITY_MACROS".

Manual changes not made by coccinelle, that were squashed in:

* Whitespace-wrap argument lists for repo_hold_locked_index(),
  repo_read_index_preload() and repo_refresh_and_write_index(), in cases
  where the line became too long after the transformation.
* Change "refresh_cache()" to "refresh_index()" in a comment in
  "builtin/update-index.c".
* For those whose call was followed by perror("<macro-name>"), change
  it to perror("<function-name>"), referring to the new function.

Signed-off-by: Ævar Arnfjörð Bjarmason <avarab@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

builtin/clean.c

@@ -6,7 +6,7 @@
  * Based on git-clean.sh by Pavel Roskin
  */
 
-#define USE_THE_INDEX_COMPATIBILITY_MACROS
+#define USE_THE_INDEX_VARIABLE
 #include "builtin.h"
 #include "cache.h"
 #include "config.h"
@@ -1012,7 +1012,7 @@ int cmd_clean(int argc, const char **argv, const char *prefix)
 	prepare_repo_settings(the_repository);
 	the_repository->settings.command_requires_full_index = 0;
 
-	if (read_cache() < 0)
+	if (repo_read_index(the_repository) < 0)
 		die(_("index file corrupt"));
 
 	pl = add_pattern_list(&dir, EXC_CMDL, "--exclude option");