To do this, we need to start Nautilus with the --no-desktop option. Start by making moving /usr/bin/nautilus to /usr/bin/nautilus.original, and create a new script at /usr/bin/nautilus containing the following command:
#!/bin/bash nautilus.original --no-desktop $@ &
The $@ expands any passed arguments, allowing the use of the script as if it were the original Nautilus binary.
To ensure Enlightenment uses only Nautilus, we need to disable the integrated file manager from the Modules settings (Run Everything -> Modules -> Files). Disable EFM (Starter) and EFM Operation Info and close the settings window.
If you use the Places module, either on the desktop or in a panel, you'll also want to ensure that this launches Nautilus instead of the integrated file manager. To do this, right-click on the gadget, then go to Settings. Finally, select Use a custom file manager and enter nautilus in the box.
And we're done - we're now using Nautilus as a replacement for the Enlightenment File Manager.
References:[Crunchbang Forums: Make nautilus --no-desktop default.]