I have an existing snapshot maven repo that I have installed Nexus "over the top" of. I am able to browse the repo via the nexus UI and I can see all of my snapshots. However, when I search the repo, the search fails to return all but 2 of the snapshots. I have encountered the same issue when creating the indexes manually using the nexus-indexer-1.0.0-beta-2-cli.jar. I've manually inspected the indexes using Luke and confirmed that it is not a complete index of my snapshot repo. In other words, the index is missing several of my snapshots. I can make available the portion of my repo that is not be properly indexed as well as the generated index, if that would help trouble shoot the issue.