TBH, I'm not sure if the following is by design, but at minimum, it needs some warning/clarification in the documentation. Mixing databases created without '--directoryperdb' and databases created with '--directoryperdb' does not work.

If a user has an existing mongod running w/o '--directoryperdb' but restarts w/ it enabled, old databases will no longer be addressable. For example, before enabling '--directoryperdb', my dbpath looks something like:

drwxr-xr-x   2 slee  wheel         68 May  8 09:41 journal
-rwxr-xr-x   1 slee  wheel          5 May  8 09:41 mongod.lock
-rw-------   1 slee  wheel   67108864 May  7 13:47 test.0
-rw-------   1 slee  wheel  134217728 May  7 13:26 test.1
-rw-------   1 slee  wheel   16777216 May  7 13:44 test.ns

Subsequently, I enable '--directoryperdb' but when I query for anything inside of the test database, mongod expects to find test's data files organized in the following fashion.

drwxr-xr-x   2 slee  wheel         68 May  8 09:41 journal
-rwxr-xr-x   1 slee  wheel          5 May  8 09:41 mongod.lock
-rw-------   1 slee  wheel   67108864 May  7 13:47 test/test.0
-rw-------   1 slee  wheel  134217728 May  7 13:26 test/test.1
-rw-------   1 slee  wheel   16777216 May  7 13:44 test/test.ns

Stopping mongod, moving the test data files into a 'test' subdirectory of the dbpath root, and starting mongod --directoryperdb seems to work (w/o any deeper testing...); I can address the test database again.

This is an important distinction because a user could want to use '--directoryperdb' to take advantage of a dbpath spanning multiple disks, but the user should be aware of having to potentially migrate existing databases before enabling '--directoryperdb'.