I'm old school, so I still like to deploy the PowerBuilder runtimes with the PowerBuilder application. The PowerBuilder runtime packagers doesn't do loose files, it either creates a single MSI or MSM file. So, to date, what I end up doing is checking the PowerBuilder Runtime Files section of the PowerBuilder documentation and cherry picking off the files I need.
Fortunately though, there's a new utility available in the Windows Store call MSI Viewer that does a bit more than just view the contents of an MSI file. In particular, it allows you to extract the original files from the MSI file. Now I can use the runtime packages to generate an MSI with the files I need and then use MSI Viewer to extract the files back out again to package with my app.