The atexit stat-index flush did an unconditional mkdir(parents=True) on the cache path, so
if the corpus/output tree was deleted during the run the flush recreated the whole
graphify-out/cache/ chain as a husk. Skip the write when the index root no longer exists
(clearing the dirty flag so nothing retries); a live run still writes, and a cold start is
unaffected because the root exists before graphify-out/ does.
