Dooom is a Doom port for the Dingoo Native OS by the_wub, which itself is based mainly on the Chocolate Doom source port by Simon Howard.

Release notes:

I’ve uploaded version 1.1 to the google code page. This version lets you put all your wads in the dooom folder with a separate command line file for each wad. The wad selector lets you select either a wad file or a command line file and I’ve changed the file format of the command line files to .txt to make editing easier with notepad!

The really important bit: You must also specify the wad needed for a total conversion or modded wad with the -iwad command line option.

So, for Aliens Total conversion I now have this:

chocolate-doom -deh atcud19.deh -merge alitcsf.wad -file alitcsnd.wad alitcwad.wad -iwad doom.wad

You can save the command line file as anything you like .txt This is a lot easier to use now but I will have a look at getting it working with wads in separate folders with a proper savegame folder for each.