when output file is overwritten CLI shows warning message, implement yes...

Fixed #38

- When output file is overwritten, CLI shows warning message
 - Now CLI functions shows warning message when they "overwrite output file", "destroy [runs, analyses]" "replace [runs, analyses]"
- add a option "yes" for all CLI functions
 - If you will answer yes to all confirmation, you can put "--yes" or "-y" option on command line like
```
 ./bin/oacis_cli create_runs -p parameter_set_ids.json -j job_parameter.json -n 1 -o run_ids.json --yes
```
Thor#sayの出力が現れるのが時々だというのも気になります。
根本的な解決ではなさそうなので、元に戻しておきましょうか？