Haha, yes! Now we're cookin'! The "simple, but naive way" you describe above is pretty much the way boot does things. I'd say you could look at the boot cljs task to see this but setting up the environment for the CLJS compiler is pretty tricky so the code there isn't as clear and elegant as I'd like.

In boot tasks don't fish around in the filesystem to find things. Not for input nor output. Tasks obtain the list of files they can access via functions: boot.core/src-files, boot.core/tgt-files, et al. These functions return immutable sets of java.io.File objects. However, these Files are usually temp files managed by boot.

Boot does things like symlinking (actually we use hard links to get structural sharing, and the files are owned by boot so we don't have cross-filesystem issues to worry about), and we shuffle around with classpath directories and pods.

So stay tuned for the write-up of the filesystem stuff, I think it might be right up your alley!