adds start/stop options and fixes restart issues

[philipwjones]

In an attempt to fix various restart issues, the methods for starting and stopping a run have been refactored. These are more fully described in the user and developer guides in the time stepping sections, but include:

• adding a config stop option to support stopping at a time, after an interval, or on a signal from coupler
• using a stop criterion string together with the stop option to determine stop time
• adding a start option to support start-up, continuation and branch runs (introduced for coupling but now moved to time stepper to simplify standalone starting as well)
• fixes some related clock and clock reset issues on restart that were impacting a number of situations, especially in streams for appended files

These changes required changes to the input config so after this PR, users/developers will need to update their config files accordingly.

Checklist

• Documentation:

  • Design document has been generated and added to the docs
  • User's Guide has been updated
  • Developer's Guide has been updated
  • Documentation has been built locally and changes look as expected

• Linting

  • Pre-commit run locally

• Building

  • CMake build does not produce any new warnings from changes in this PR

• Testing

  aurora, oneapi-ifx, mpich

  • CTests Pass
  • Polaris omega_pr Pass

  chrysalis, oneapi-ifx, openmpi

  • CTests Pass
  • Polaris omega_pr Pass

  frontier, craygnu, mpich

  • CTests Pass
  • Polaris omega_pr Pass

  frontier, craygnu-mphipcc, mpich

  • CTests Pass
  • Polaris omega_pr Pass

  pm-cpu, gnu, mpich

  • CTests Pass
  • Polaris omega_pr Pass

  pm-gpu, gnugpu, mpich

  • CTests Pass
  • Polaris omega_pr Pass

• Provide relevant details in a comment to the PR titled Testing with the following:

  • Which machines CTest unit tests
    have been run on and indicate that are all passing.
  • The Polaris omega_pr test suite
    has passed, using the Polaris e3sm_submodules/Omega baseline
  • Document machine(s), compiler(s), and the build path(s) used for -p for both the baseline (Polaris e3sm_submodules/Omega) and the PR build
  • Indicate "All tests passed" or document failing tests
  • Document testing used to verify the changes including any tests that are added/modified/impacted.

Fixes #482

[philipwjones]

Passes Ctests on Chrysalis. I also tested running 5 days and restarting for another 5 days and verified that the append option works to correctly write daily time slices to a single file (to verify fixing #482)

[philipwjones]

omega-buildnml PR tests are failing due to changes in the config file needed for this PR.

[philipwjones]

I will be mostly out of contact for about two weeks starting 8/25. I might be able to briefly respond to any issues and point to fixes but will not be able to access/modify code during that time.

[xylar]

@philipwjones, just a quick note to say that I have seen this work is up and I really appreciate it! I'll get to reviewing it as soon as I can.