There's no dedicated tutorial on how to perform a palette fix in Gimp, so I decided to make one.
Step 1. Have Gimp installed on your computer.
It is cross-platform, so you shouldn't have a problem getting a binary. If you're too lazy to search for it, here's some links.
Gimp main site
Windows binary
Mac-OSX binary
Linux: You should either have it or be able to figure it out yourself. I know the ubuntu software thingy has it, and I'm sure you can grab it from apt-get.
Step 2. Have the palettes to install.
The palettes can be found here on the forum, or if that link goes bad, here (and here) on mediafire.
Step 3. Install the palettes into your Gimp directory.
For any of the three OS's, open up Gimp and head to Edit -> Preferences. There should be an item to the left that says "Folders", and under that "Palettes".
There it should list where it looks for palettes by default, and if you like you can specify a new one. Remember, copy, or write down the path you will install the palettes to, and exit Gimp.
Go to that folder and put the two .gpl files in, and restart Gimp.
Step 4. Load the image you wish to place in palette.
If you do not already have it in your floater, you can place the Colormap tab into the floater to the right by clicking on the small left-pointing arrow near the top of the floater (below the other tabs), and selecting the "Add tab" -> "Colormap" menu item.
If you had saved this from another program that automatically creates optimized palettes for saved images, you will see some color swatches already in the colormap tab. If it's non-indexed, it will simply be blank with a message to the effect of "Only indexed images have a colormap".Step 5. Convert your image to an indexed image.
This is the hardest step since you have to remember to have a few options enabled. Once your image is loaded, click on the menu items Image -> Mode -> Indexed. If your image is in palette, Indexed will have a dot or a check or something by it already, and you will have to click on RGB, then do it over again to get back to Indexed.
This will open up the Indexing dialog, where you specify how you want to index your image. Select the "Use Custom Palette" radio button, and from the drop down activated by the button right below the radio button, select the palette you'd like to use. If you're doing anything other than terrain or bunker modules, you'll want the Cortex Command palette (as opposed to Cortex Terrain). Make sure that the "Remove Unused Colors" checkbox is unchecked, with no dithering, and hit the OK button.
Step 6. Finally, check that everything went as planned.
If you've followed the instructions correctly, the Colormap tab should show a palette of 256 colors (indices 0 to 255), beginning with magenta and ending with a blackish color, and your image should look pretty much the same as it did (perhaps minus a few colors and looking somewhat more 8-bit).
Save your file as you like and you're done!
