_api is an internal config package and must not be modified by the user on disk. The core handles the files in there in a proper way.
You also do not place files directly to the package path on disk, but just use the REST API endpoints for that.
conf.d is static configuration just for this node,
zones.d needs the zone directory underneath - in the same way as you would manually put files into
The core uses a package path prefix on its own, this may change in the future (including migrations). So don’t write scripts which rely on
/var/lib/icinga2/api/packages or something similar.