I am interested in protecting my Due after programming. The datasheet talks about the "Security Bit Feature" (section 18.104.22.168) that can be used for this.
Has anyone done this by any change? Does anyone have example code?
To answer my own question: I enabled the 'Verbose Uploading' feature in the IDE and I see that the 'bossac' tool is used for uploading. One of the parameters to this tool is the '-e' option, which enabled the flash security flag.
So I think I can simply manually execute this command after compiling the code.