Keep standalone CIME case output in the Omega build directory

[xylar]

Standalone builds now keep the throwaway CIME case's bld and run directories inside their own build directory by passing --output-root to create_newcase. Before this, every standalone build by a user on a machine shared $CIME_OUTPUT_ROOT/e3smcase/{bld,run}, so builds configured at the same time could delete each other's directories.

Fixes #581

Checklist

• Linting

  • Pre-commit run locally

• Building

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

• Testing

  chrysalis, intel, openmpi

  • CTests Pass

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

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Posted by Claude Code on @xylar's behalf. The testing, analysis and wording above are AI-authored; please check them accordingly.

🤖 Generated with Claude Code

[xylar]

Testing

CTests pass (50/50) on Chrysalis with Intel and OpenMPI from a clean build of 415422d in:

/gpfs/fs1/home/ac.xylar/e3sm_work/polaris/main/build_omega/build_chrysalis_intel

Two standalone configures started at the same time on Chrysalis both succeeded, each with the case's bld and run inside its own build directory.

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Posted by Claude Code on @xylar's behalf. The testing, analysis and wording above are AI-authored; please check them accordingly.

[andrewdnolan]

This seems like a very sensible change to me. I haven't had a chance to test myself, but approving based on code inspection and @xylar's testing.

[xylar]

@grnydawn, could you also please give this a quick look?

[grnydawn]

This resolves a long-standing issue. I briefly verified that a separate build directory is created for each Omega build. Approved.

[xylar]

Thanks @grnydawn!