The problem is the CWAF tool is notoriously buggy. It misses project files, and it's also deleted audio it shouldn't. Which makes it untrustworthy.
 
Save As and Copy Audio is the way to go, but there's no way to batch that so you have to open every project file in existence in one physical session (or keep copious notes) in order to complete the process. Ugh!

This would be a nice feature request. A batch function that could drill into a select folder (especially the global audio one), then run a "save as" on ALL .wrk, .cwp files to auto name a new folder with the project file name to comply with the current per project folder layout. If already existing, would need to prompt the user for an overwrite or not. This has application now since "new project" without choosing a project name dumps everything into the global audio until a save is performed (and then only copies AFAICT).

...wicked
The problem is the CWAF tool is notoriously buggy. It misses project files, and it's also deleted audio it shouldn't. Which makes it untrustworthy.

Say what ???
I don't think so. The clean audio folder tool can take for ever + a life time but the CWAF tool has been solid.
then again I know what I am deleting and what I need to save. because I read the list before I hit "Delete all".
 
CWAF only lists what you want to remove, it is up to the end user to choose to delete them or not.
is this what you mean by notoriously buggy?
Matter of fact I cant even return any searches on Google that say the CWAF tool is buggy, or doesn't work.
with all this being said, The clean audio folder and CWAF tool both need an update to make them more modern.
Slow, outdated...yes.
Buggy ? no.