Improve run_sys_tests behavior when baseline directories already exist

When a user does `run_sys_tests ... --generate /some/existing/directory`, the submission seems to work (i.e., that command succeeds). However, any test whose baseline already exists there will fail, with the `STDERR` file saying `Use -o to avoid this error`. That message is from `cime/scripts/create_test.py`, but this isn't obvious to the user, who may then try `run_sys_tests ... --generate /some/existing/directory -o`. This doesn't work, as `-o` isn't an accepted option of `run_sys_tests`.

I think it would be better to handle this sort of situation upon the call of `run_sys_tests` itself.

Possible mitigations:
1. ~~Throw an error if the directory specified by `--generate` already exists.~~ This would be really annoying in the case where the user is only running tests whose baselines don't already exist there, so I don't consider it a real option.
2. Add `-o` as an option of `run_sys_tests`. We may not _want_ to allow this, though, as it could be unintentionally destructive.
3. As 2, but print the baselines that already exist and ask for confirmation.