I am using Ubuntu 13.04 with Django 1.5.1 and Eclipse Juno. Whenever I try to create a project via the terminal using
django-admin.py startproject <projectname>
and then If I try to import it to Eclipse, by creating a new project in the workspace, it screws up the directory structure of my app.
To overcome this, I create project from eclipse using the standard eclipse "create project" dialog. After that I can go about my usual business.