This won't always clean the intermed directory

Line 75 in 4d5e543

    
           if(file.exists(paste0(out.path,"/intermed"))) system(paste0("rm -f ", out.path, "/intermed/", run.label, "_", "*.summary;"))

If I do one run call sebastes_testing, and then I do another run called sebastes then it looks like the outputs from the first run will still be around in the directory and then will get bunged into all.summary.

Why not just remove the entire directory intermed and then remake it each time? It seems that would be safer unless there is something that would break.

issue is resolved. Any files in intermed will be removed before populating with new intermed files