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I have no problem with the backup/testing files. I guess I just fail to see how a totally new file should be placed ONLY in the template_default while other files are placed in the YOUR_TEMPLATE.
Is there an instance where a file might ONLY be needed for backup/testing?
Part of the original reason for broaching the subject is that we have folks that purge classic and template_default thinking they're going to get some SEO benefit from getting rid of the extra files. Especially the css.
The approach I've taken (lately) with my plugins is to put any new files into /template_default and any template-override files (i.e. built-in ZC files modified) into the YOUR_TEMPLATE directory. That includes any .css/jscript files since those require presence in the currently active template directory.
You could argue that completely new functionality/pages may go in template_default, but modifications to existing functions/pages should use overrides.
As far as I am concerned, an upgrade is always an entire fileset comparison, there is always some housekeeping duties that it throws up, so stuff should not get missed because it is in unexpected places, in fact it should be more noticeable: new files in template_default stick out like a sore thumb.