The ensure_index paster command misses some indexes:
CommitRunDoc which uses the repo_commitrun collection doesn't get its indexes created, because there is no mapper(...) line for it at the bottom of allura/Allura/allura/model/repository.py. (There is no class to map it to currently)
Also the activitystream indexes on activities and nodes don'te get created, despite code in EnsureIndexCommand that uses activity_odm_session to try to do so. Must be a bug in it.