Just looking through my site's files, it seems that 5.4.0.2 is 'installed' in its entirety in /c5root/updates/concrete5.4.0.2. Why is this? Why isn't the original overwritten? Does it mean that for further updates there will be multiple directories in the updates/ folder with full installations, taking up lots of space?
This is important because it's not clear where to make changes to core files now - do we save them in the 'root' c5 (the initially empty set of directories), or in the update, or in the older version? It's not clear.