apply: only write intents to add for new files

In the "apply only to files" mode (i.e., neither --index nor --cached
mode), the index should not be touched except to record intents to
add when --intent-to-add is on. Because having --intent-to-add on sets
update_index, to indicate that we may touch the index, we can't rely
only on that flag in create_file() (which is called to write both new
files and updated files) to decide whether to write an index entry;
if we did, we would write an index entry for every file being patched
(which would moreover be an intent-to-add entry despite not being a
new file, because we are going to turn on the CE_INTENT_TO_ADD flag
in add_index_entry() if we enter it here and ita_only is true).

To decide whether to touch the index, we need to check the
specific reason the index would be updated, rather than merely
their aggregate in the update_index flag. Because we have already
entered write_out_results() and are performing writes, we know that
state->apply is true. If state->check_index is additionally true, we
are in --index or --cached mode, which updates the index and should
always write, whereas if we are merely in ita_only mode we must only
write if the patch is a new file creation patch.

Signed-off-by: Raymond E. Pasco <ray@ameretat.dev>
Signed-off-by: Junio C Hamano <gitster@pobox.com>