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>

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