Method 1: GIMP
Method 2: Bash script (Recommended)
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Step 3 - Noggit Red Setup
Launch Noggit Red and create a new project.
Create a new map named Mountains with 10x10 ADTs starting at 1-1.(Set the map expansion to latest for maximum in-game view distance.)
Copy the heightmap and alphamap tiles into your Noggit Red project folder at "/world/maps/mountains/".
(The folder contents should look like this, with one heightmap and three alphamaps for each ADT.)
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Step 4 - Importing the Heightmap
Enter your map in Noggit Red and import the heightmaps with Assist > Global > Import > Import heightmaps using a multiplier of 3000.
(You can play around with the multiplier to increase or decrease the vertical "stretch" of the terrain.)
The terrain should now be deformed.
Load all ADTs with Assist > Global > Debug > Load all tiles
Reset the lighting and shadows on the terrain by using a sculpting tool with maximum brush size and 0.00 speed.
Fix gaps in the terrain with Assist > Loaded ADTs > Fix gaps
If you come across impassable tiles, go into Impass Designator mode and use ctrl+left click on the greyed-out squares.
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Step 5 - Applying Texture Layers
Press U to enter tile mode and zoom out so you can see the entire map.(If you see black spots on your map in tile mode, go back to the normal view and raise your camera height with Q.)
Using the largest brush possible, paint your map with a base texture at 100% opacity. I used rock.
Repeat the process with a second texture. This is the texture that will be masked off by your layer1 alphamap. I used soil
Repeat the process with a third texture. This is the texture that will be masked off by your layer2 alphamap. I used grass.
Repeat the process with a fourth texture. This is the texture that will be masked off by your layer3 alphamap. I used sand.
In Texture Painter mode, ctrl+click somewhere on your terrain to bring up the texture picker. You should see 4 textures.
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A Note on Alphamapping
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Step 6 - Importing the Alphamaps
Import the alphamaps with Assist > Global > Import > Import alphamaps. After everything loads you should see the final product.