The commonality to which I referred is for the one application only. (That may be what you were implying, not across all applications.) But the subtransform approach is still valid in this case. Thanks for the idea.
I feel that I have not explained clearly enough the Studio features that we use. We often export classes to XML files. Similarly, we import XML files, compiling them as classes during import. I didn't mean to imply that this was done simply to transfer classes to other namespaces or servers. Rather, it's a way to archive classes as XML files. (We don't use a source control system.)
We use the Find in Files utility to determine the classes and other files in which a given string exists.
I mentioned the Namespace variation of the Studio Workspace pane because that is the arrangement of files (classes, lookup tables, message schemas, etc.) that we most often use.
We sometimes export classes from one environment and import them to another. I don't see .cls as a supported file type for those activities.