In this article, I am going to tell you how to delete files for ever (almost) in Nautilus using a command-line tool and also, how to add this functionality to Nautilus, when right clicking a file / folder. First, I would like to thank Gnome Tips for their Shred article.
Using Shred from a terminal
To delete a file from a terminal, use the following command:
shred -f -v -z -u file_to_delete.zip
Where,
-f : changes the permissions to allow writing if necessary
-v : to show the progress
-z : add trailing zeros to hide shredding
-u : remove the file after overwriting
Adding Shred to Nautilus context menu
sudo apt-get install nautilus-actions
Then, go to System -> Preferences -> Nautilus Actions Configuration and click "Add" and fill in the Name, Tooltip and Icon fields as you wish. Here are mine:

Now, select the "Main" profile and click "Edit" and:

-in the "Path" field, enter:
shred
-in the "Parameters" field, enter:
-f -u -v -z %M
Then, on the "Conditions" tab, under "Appears if selection contains" select "Both", and also check the "Appears if selection has multiple files or folders" box:

Click "OK". We are now finished with this.
Now, we must restart Nautilus. Open a terminal and paste this:
nautilus -q
Then start Nautilus by pressing ALT + F2 and entering:
nautilus