Currently we have an extremely confusing situation with SolrCloud configuration management. SolrCloud expects its collection configs to be available in Zookeeper and treats the configs in the local file system as seed for the ZK copy only.
Thus we have an unfortunate situation where an unsuspecting sysadm will happily modify settings under /etc/solr/conf/<collection>/ and be very frustrated by SolrCloud not taking the values in.
NOTE1: as I mentioned – this only applies to collection configs. For example /etc/solr/conf/solr.xml is fine.
NOTE2: also note, that even though in Bigtop context SolrCloud configuration makes more sense than a standalone Solr server it is completely possible for folks to run Solr in a standalone mode as well. In which case you have to have local configuration files under /etc/solr/conf/<collection>/ since ZK is not being used.