Include rules enable transforms to be spread across multiple files and subsets reused by different manifests. Suppose you need to deliver two packages: A and B. Both packages should have their source-url set to the same URL, but only package B should have its files in /etc set to be group=sys.
The manifest for package A should specify an include rule that pulls in the file with the source-url transform. The manifest for package B should specify an include rule that pulls in the file containing the file group setting transform. Finally, an include rule that pulls in the file with the source-url transform should be added either to either package B or to the file with the transform that sets the group.