This menu groups operations which apply only to images.
To use Rotate / Straighten, mark an arrow on an image (Ctrl-drag up and left in an image view window) along a near-horizontal or near-vertical edge. When you click on Rotate / Straighten, nip2 will rotate the image by the smallest amount that makes that edge exactly horizontal or vertical.
Linear Match takes two images and rotates and scales the second so that the images can be superimposed. Drag the tie-=points to mark common features. Use Filter / Overlay or Filter / Colourize to actually superimpose them.
Rubber Sheet is useful for fixing things like lens distortion. You give Find two images, a reference and a distorted version of that reference, and it automatically finds a transform which will map the distorted image back on to the reference image. Use Apply to apply the discovered transform to another image.