Changes

Summary

1. proper file extension for Isabelle_System.extract;
2. tuned implementation;
3. more uniform use of make_directory;
4. tuned message;
5. tuned: less redundant implementation;
6. clarified signature: copy directory content more directly;
7. more robust;
8. tuned whitespace;
9. clarified signature: more general operations;
10. clarified signature;
11. tuned signature;