With the old engine, you could shift folders/files in and out and they would become immediately available for access from clients.
This was a great way to manage large data importing / index rebuilding. You could take a single server offline - build new data/indexes and then systematically copy this structure around ones replicaset to get them back into sync - oplog - didnt come into it.
With WiredTiger engine, this will not work, as if you create a new database/folder or increase the collection count within that database - it is ignored.
I believe because the underlying structure is not generated to support the new files.

Is it possible to generate this missing structure simply by issueing a command which would then parse the file structure to rebuild its internal mappings.

Hope that explains the requirement. Sorry if this request is already somewhere else - its a little fiddly to find through Jira.