@burhansalih Ok, this is how I had always understood it up to now.
@Homlet Do you think it is possible and useful to (optionally) automate the deleting process of the atmosphere folder using aio-updater? SciresM also always recommends deleting the atmosphere folder before updating. And I think,
@deejaybenji would not have got the SSB crashing bug, if he always deleted his atmosphere folder before updating.
To keep the sysmodules, users could create a custom folder somewhere on the sd containing their sysmodules and use the copy_files.txt to automate the copy process of the sysmodules after updating.
Using this method, the aio-updater would combine a very clean and a very comfortable method to update atmosphere.