Saving (platform-independent) files to a different directory in the filesystem with Clojure turned out to be a bit more difficult to track down than I expected, though the solution is simple enough.
For a platform-independent approach, you can find the canonical path from a path relative to the project and then join it with the filename.
(:require [clojure.java.io :as io :refer [file]])
(defn file-dir
"Returns canonical path of a given path"
[path]
(.getCanonicalPath (io/file path)))
(-> "./resources" ;; relative
(file-dir)
(io/file "filename.txt")) ;;=> /path/to/project/resources/filename.txt