For the windows files, I would prefer one lightweight .exe with all media embedded, that runs in it's own "virtual machine" in memory, just like when you pack it with the smartpacker program.
When it comes to the ios, here is a tip:
To make a IPA the easy way...........
Step 1. download winrar or winzip and install it
Step 2. download any IPA
Step 3. right click on your IPA and select properties
Step 4. change the (open with program) to winrar-winzip click ok
Step 5. dbl click your IPA
Step 6. delete artwork and replace with yours
Step 7. delete folder payload and replace with yours
Step 8. close IPA and change the open with program back to itunes
Step 9. rename your IPA the title of the program your installing - done
Don't know about the certificates though...
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AGK programmer
Did Amiga / AMOS programming in the 90's.