trivial refactoring
run job from work_dir

- job is executed at run_dir
  - job script must not have cd #{run_id};
  - however, for manual_submission, cd #{run_id} is necessary.
  - therefore, 'if' statement to detect manual_submission is inserted
- scheduler log files are located at work_base_dir (not work_dir)
  - so add options to print scheduelr logs to work_base_dir
spec maintenance
add test for xsub