xconf files should be installed into /db/system/config, this is how indices are created. The pre-install.xql script already copies /db/apps/grammateus/collection.xconf there, so that collection is always indexed when installing the xar.
However, /db/apps/grammateus/data/papyri/collection.xconf must be installed from the post-install.xql script because it uses a grammateus module that must be installed before copying that xconf into /db/system/config.
Finally, the collection must be reindexed because the indexed documents have been copied into the db before index creation.