Remove extensions of embedded tools.

[phillebaba]

Describe what should be investigated or refactored

In #1966 when implementing the prune command we chose to put it in the crane embedded tool command path. One reason for this may be because both zarf tools registry and zarf tools crane calls the same code internally. It makes little sense to extend on the functionality of a tool that we have embedded. In theory we have forked crane with out own functionality. This should be moved to some other command instead.

Links to any relevant code

https://github.com/zarf-dev/zarf/blob/d7eb999851bc20ac68155fe11a23ed2b151a975d/src/cmd/tools/crane.go#L69-L74

Additional context

N/A