The --update path excluded config.env from the safe_copy_tree, which
meant new config vars added to spec.yml were never written to
config.env. The XXX comment already flagged this as broken.
Remove config.env from exclude_patterns so --update regenerates it
from spec.yml like the non-update path does.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>