src/Pure/Admin/build_history.scala

 
       /* next build */
 
       if (multicore_base && first_build && isabelle_output_log.is_dir)
         Isabelle_System.copy_dir(isabelle_output_log, isabelle_base_log)
+
+      Isabelle_System.rm_tree(isabelle_output)
 
       first_build = false
 
       (res, log_path)
     }

         File.bash_string(isabelle_admin + "/build_history") + " " + options + " " +
           File.bash_string(ssh.remote_path(isabelle_repos_other)) + " " + args,
         progress_stderr = progress.echo(_)).check
 
     for (line <- result.out_lines; log = Path.explode(line))
-      yield (log.base.implode, ssh.read_bytes(log))
+    yield {
+      val bytes = ssh.read_bytes(log)
+      ssh.rm(log)
+      (log.base.implode, bytes)
+    }
   }
 }