I found it strange aswell that it was missing but it makes sense.
You should rename all sub files aswell (layout files, code modules, classes) when you do an updated/new version
as these will change aswell.
So I guess this leaves 3 options.
1. copy the folder to a new folder (myapp\1.0 -> myapp\1.1 or so)
2. export to zip before you change anything
3. use a svn/git tool to track version changes.
1 is the easiest, 3 the most usefull I guess as you can easily compare them to find screw ups