`crossplane beta convert` commands do not preserve comments and keys ordering

### What problem are you facing?

Currently all `crossplane beta convert` subcommands write to disk stripping comments and keys ordering, requiring manual intervention to restore the manifests after a migration. This is clearly sub optimal, however the solution is not so straightforward.

### How could Crossplane help solve your problem?

We currently parse manifests, rework them, marshal them to YAML and write them to the specified output location. To preserve comments we'd have to parse the manifests as `gopkg.in/yaml.v3` as `yaml.Node` and move nodes around as needed.