What algorithm is used to get the centroid clusters? Do you need to know the number of clusters in advance? I am familiar with max-link/min-link/avg-link hierarchical algorithms, but not centroid related ones.
We represent clusters as a type of node. So if your other nodes have coordinates in a space, there will be distances between your clusters. Or they can be part of a graph traversal, etc.
Can you be more specific about the cluster membership testing? Sure it is based on some "distance" calculation, but how do you avoid long chain problems inherent to clustering algorithms? And to reiterate, do you need to know the number of clusters ahead of time?