In the post at the link below about clipping it says: " It doesn't change the input data though, but actually outputs a new dataset with the portion of the input data that overlaps the clipping feature."
how-to-cut-a-rectangle-out-of-a-shape-file
If I have a map with 5 shape files. I create a rectangle that covers a portion of the map. I clip all layers to the extent of the rectangle. Now, only a portion of the source shape files is visible. The original input shape files remain the same. When I save the project, does it output a new set of shape files somewhere? When I close and re-open the project the source of the shapefile layers is still the same original large files. What I am trying to do is create new smaller shape files that match the extent of the rectangle. The map I am working with is huge and I would like to create a new map that is a smaller portion of the original map.