Create one logger object per instantiated Run() object and fix logger not including full traceback

[tomvothecoder]

Description

• Closes [Bug]: e3sm_diags_run.log was not properly generated  #848
• Closes [Bug]: prov log doesn't include complete traceback #909

What we need

• One logger module saved to file per simulation
• All logger outputs for one simulation saved to a file (via append)
  • Works with serial -- works
  • Works with multiprocess -- blank file
• Save log directly to prov instead of waiting for run to end (makes debugging harder)

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

If applicable:

• New and existing unit tests pass with my changes (locally and CI/CD build)
• I have added tests that prove my fix is effective or that my feature works
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have noted that this is a breaking change for a major release (fix or feature that would cause existing functionality to not work as expected)

[chengzhuzhang]

@tomvothecoder Another thing that bothers me a little, is that the e3sm_diags_run.log file was created in the directory where the run script is located, I'm wondering if it makes more sense to have it initiate under /prov, right away?