In the IDD you need to tell it which gaps you want to zip.
There are 2 different gaps tools. One under the repair mode and one under the featurize mode.
Repair mode:
Use the search tool to find “gaps”. You can then increase the size until you have them all. This is a lot like the old tool. While they are selected you need to add them to the wire frame. Then use the repair tool.
Featurize:
Choose the define gaps tool. Pick each side of the gap in the appropriate box. Then use the close tool. (You could use the search tool here as well).