Since today’s snapshot build #579, you will notice that files have been moved around (see details here), so you might have some hick-ups doing upgrades from previous snapshots (the apt package most likely does not yet work for an apt upgrade, sorry for that).
The good news is: The new folder layout should solve many issues in future regarding the upgrade process. All configuration that is stored in OSGi ConfigAdmin (e.g. settings that are done through Paper UI) are not lost anymore as they are now within the userdata folder, which does not get overwritten. Same is true for the logging configuration, which is not lost anymore.
Another folder that moved out of “runtime” is “sounds” - this can now be found in
conf/sounds instead, see here.
As a result, the content of the runtime folder should be completely uninteresting for any user - there should be no need to ever touch any file; if you do not agree, please let me know!
This is a vital part of the concept: Having the runtime folder completely read-only (e.g. mountable on a read-only file system as well) and being able to fully replace it by updated versions without having to care for any user changes.