We first restart in-progress indexes: https://github.com/mongodb/mongo/blob/a08d6998928720aeea25546dca785f242b6b102d/src/mongo/db/db.cpp#L926 , and then we start replication: https://github.com/mongodb/mongo/blob/a08d6998928720aeea25546dca785f242b6b102d/src/mongo/db/db.cpp#L958
, which is where we check for initial sync. Creating indexes can take a very long time and we should skip this if we're going to go into initial sync immediately.