Make PPM safer to use when using overlay (fixes #3188) #3317
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Modification of lower layers leads to undefined behavior under overlay, so applications must be installed to / and removed from /. This ensures whiteout files in pup_rw are created correctly, and snapmergepuppy.overlay synchronizes the installed/removed package to pup_ro1.
In addition to the extra safety, it's nice to be able to install or remove a package and reboot without saving the changes if you regret what you did.