Make Azul indexer handle a mix of skunk and normal bundles

[hannes-ucsc]

This is necessary if we ever want to put our special skunk bundles (one bundle with one matrix per project) into the integration, staging or prod deployments of the DSS.

This also entails deciding which commits on the skunk branch should land on develop and which ones should be discarded. I've added a few commits with KEEP and KEEP? in the commit title to the skunk branch.