|Do not use absolute pathnames in your paper directory; always make relative references to files within your paper directory.|
Ideally , if you followed all guidelines so far, you should have a paper directory that can be moved in its entirety without breaking anything. In that case it takes a mere cp -r of your paper directory paper1 in order to include it in a report or book as username1.
cp -rp /myhome/paper1 /report_directory/username1
After copying go ahead and test if your Cakefile is able to generate all figures and make sure the actual data files are within your paper directory and not on some scratch directory. (You will not have to worry about that if all your file references (especially data files) are relative. Go to your paper directory and type cake burn. That will remove all rebuildable figures. Thereafter you can test if all figures rebuild ok, by typing cake figures.
Try to make your figures interactive (bring up movies, etc.). By default, when you click a button on any figure, a menu will come up that lets you choose some action.