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Currently, Atoms provides no way of updating the containers or chroots without going into the containers.
Describe the solution you'd like
Distrobox provides a way of updating its containers using distrobox upgrade. Chroots are a bit different, but I can imagine it wouldn't be too hard to implement. Ideally, there would be an update all button somewhere, and in the Dashboard of an atom, you could choose to update that specific atom only.