Improvements for limactl prune, to not delete everything

### Description

Can be good to keep _some_ images around, for instance:

* those that are "in use" by a currently running instance, even though the actual files have been copied from the cache

* those that are referenced by the current version of a template, while pruning the old and obsolete earlier versions

When not removing the entire cache, maybe also remove:

* temporary files (data.tmp) left by previous aborted downloads

* obsolete versions of nerdctl-full, or other cached images/packages

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Partial implementations:

* #1409