Perhaps I'm doing something wrong. Current release of cameyo, Win7sp1, 64 bit. Packaged a simple application in "ghost installer mode".
Change registry handling to clean up, leaving no trace, and ask for confirmation on delete. Save (different .exe file name, or over-writing original, doesn't matter). New executable still leaves a huge VOS folder filled with stuff upon exit, and no prompt for confirmation.
Edited registry and file system, deleting unused stuff. Save (different .exe file name, or over-writing original, doesn't matter). Upon re-opening the new saved .exe with package editor, all the deleted registry keys and files are still there.
Upon loading virtual exe into package editor, it shows the icon for cameyo.exe instead of the app. Fix that manually by pointing to the app's real executable file and save (original or renamed .exe, same difference). Under Windows file manager, the icon is now correct, but if I re-load the executable into the Package Editor, it still shows the icon for cameyo.exe instead of the one I just added.
When saving a package modified with the package editor, without fail the new .exe is exactly the same size as the original - even if adding or removing stuff.