The Merge Nodes tool enables you to merge coincident nodes, manually, to improve their aspect ratio.
Assume you have two nodes, A and B, and you want to merge them into a single node.
Using the Merge Nodes tool, you can merge node B to A, or you can merge node A to B, depending on what you select in the dialog.
There is another option, Merge to midpoint, which merges to the midpoint between A and B.