In transitioning_replica_sets_jscore_passthrough suite we run a replicaset started as --shardsvr but not part of a cluster. This transition state is valid, and we should be able to execute commands.
There is a test failing though in this suite, please investigate it and remove the exclusion of the test from the suite if possible.

failing tests:

jstests/core/query/find_with_resume_after_param.js