run-fly: fix permission errors and copy directory for each run
run-fly: fix permission errors and copy directory for each run

thelmuth/Clojush,Vaguery/Clojush,saulshanabrook/Clojush,NicMcPhee/Clojush,saulshanabrook/Clojush,lspector/Clojush,Vaguery/Clojush,lspector/Clojush,NicMcPhee/Clojush,thelmuth/Clojush