Background indexing on secondaries and orphaned document cleanup in MongoDB 2.6` introduces two significant changes aimed at improving replica set robustness and reducing potential issues with secondary reads. First, background index builds on primaries are now also applied to secondaries, making it more intuitive and reducing the impact of indexing operations on the replica set. This change is particularly beneficial for users who rely on secondary reads, as it ensures that indexing operations do not affect the availability of their application. Second, a new administrative command `cleanupOrphaned()` has been implemented to remove orphaned documents from shards in sharded clusters, addressing issues related to incorrect results and data inconsistencies caused by stale copies of documents remaining on shards. These changes are available for testing in the 2.5.4 Development Release and will be feature complete with the upcoming 2.6 release.