Several classes in harness code do not have access to a logger

[hagertnl]

Files within the harness/machine_types directory do not have access to a logger, and do all messaging through print(). Some of these messages should certainly be logged at a lower threshold than what print provides. Recommend passing the apptest logger into each machine type.

[hagertnl]

For example, a scheduler (ie, lsf.py) will always print the command & return code of the command used to submit the job. This is useful most of the time, but it's also not logged to a log file, so once you leave the current screen, you will never see it again.

[hagertnl]

List of classes/files without access to a logger that would benefit from access to a logger:

• machine_types/*
• libraries/rgt_utilities.py (needed especially for set_harness_environment. This causes a lot of extra output)
• libraries/config_file.py
• libraries/input_files.py
• do_application_tasks in libraries/apptest.py

[hagertnl]

These were identified through work in PR #114 , but are not fixed in this PR.