@Stefan
@Jason
A couple things as they relate to deploying custom solutions. The Copy-SPSideBySideFiles script only copies css, js, and htm files. Which is a problem for us because we have other file types in our layouts directory that aren’t copied over. I can deploy directly to the CU specific folder by changing the deployment location and folder name of the layouts folder properties in the solution, but this is mistake prone as you’ll have to do this to every solution and make sure you have the right folder every time you deploy a solution.
I ended up running a diff of the two folders and it appears that the CU process updates both folders (…\TEMPLATE\LAYOUTS\16.0.xxxx.xxxx\ and …\TEMPLATE\LAYOUTS\) with the same changes, which I wasn’t aware of. So, instead of changing the Web App SideBySide token to point to the new folder, just leave it alone, or set it to an empty string if you’ve already changed it. This will load the files from your layouts folder instead of the new CU specific. You don’t have to change your deployment process and can still update with zero downtime. The only caveat is that some users may see cached versions of updated files because the file path/name is not changing.
Dan