The new background color is now user-configurable (was previously hard-coded to an ugly shade of yellow).
The output file format (PNG, JPEG, etc.) is now user-configurable.
Updated documentation to include contact information.
Remaining issues: Sprite Maker will not automatically detect where the sprite starts in both images; they need to start at exactly the same pixel location. That is, each needs to be cropped exactly the same, to the pixel.
