To answer your question... you're putting the cart before the horse, my friend. Go read the tutorials discussing how to implement a new ship first... then crabtree's tutorial. You won't understand the references to the various file types used to make a ship mod until you understand the process that we go through to make ships, which can be broken down into these steps:
1. Make model and skin in a 3D software package/paint program.
2. Export a CMP and MAT file, containing the model and the skin, respectively.
3. Create/rename/modify a SUR file, which is used to implement hitboxes for FL ships (among other duties).
4. Create the ship's entries in the relevant INI files, either through INI editing or through writing an XML script for use with FLMM
If you don't understand steps 1 through 3... then you're going to get stuck a lot on 4. Go read Drizzt's ship-making tutorial... it'll at least get you started