In using SQL Developer 4 Early Adopter version 3, I was attempting to set up an External Table. I created the appropriate directory object, but it did not appear in the pulldown for default directory in the create External Table dialogue. I was able to proceed using SQL Developer 3.2. Once I created the table in SQL Developer 3.2, I was able to edit it in SQL Developer 4.
There is a bug here in that the Dialog for the default directory should not include default directory schema (which for me defaults to the connected one). As a workaround if you change that default directory schema to SYS in the drop down then you should see your directory.