stash: make sure to write refreshed cache

When converting stash into C, calls to 'git update-index --refresh' were replaced with the 'refresh_cache()' function. That is fine as long as the index is only needed in-core, and not re-read from disk. However in many cases we do actually need the refreshed index to be written to disk, for example 'merge_recursive_generic()' discards the in-core index before re-reading it from disk, and in the case of 'apply --quiet', the 'refresh_cache()' we currently have is pointless without writing the index to disk. Always write the index after refreshing it to ensure there are no regressions in this compared to the scripted stash. In the future we can consider avoiding the write where possible after making sure none of the subsequent calls actually need the refreshed cache, and it is not expected to be refreshed after stash exits or it is written somewhere else already. Reported-by: Jeff King <peff@peff.net> Signed-off-by: Thomas Gummerer <t.gummerer@gmail.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>