Thanks for the reply. For the time being, we're working around the issue by manually checking to see if the destination folder for the plugin contains "destination", and, if so, adjust the expected inputFiles parameter of Command.buildCommand accordingly. Clearly, this will break when further changes are made to the output folder layout, which will again strand our users with a broken project.
What is the recommended way for a plugin on target B to reference files that were output by dependent target A? The pluginGeneratedSources referenced in the Xcode release notes sounded promising, but it doesn't actually seem to exist in the current PackagePlugin module.