Refactor Slice 2: Move batch/scheduler logic into `CIME/core/batch/`

[jasonb5]

Part of #4950. Slice 2 of 5. Estimated 4 weeks. Depends on #4996.

Goal

Move batch logic from scattered locations (XML/env_batch.py,
case/case_submit.py, utils.py) into a coherent CIME/core/batch/ package.
Existing entrypoints become thin wrappers.

Why

EnvBatch (XML/env_batch.py, 1590 lines, 43 methods) is the second-largest
class in CIME. It handles batch config parsing, job submission, queue
management, and directive generation all in one class. Submission logic is
also smeared into case_submit.py and utils.py.

Tasks

Decompose EnvBatch

• CIME/core/batch/config.py — batch config / queue parsing.
• CIME/core/batch/submit.py — job submission logic (consumes from
  EnvBatch and case_submit.py).
• CIME/core/batch/directives.py — directive generation.
• EnvBatch becomes a thinner wrapper delegating to the above.

Scheduler protocol

• Define Scheduler protocol in CIME/core/batch/scheduler.py.
  PBS, Slurm, LSF are genuine polymorphic backends — DI is warranted here.
• Concrete implementations: PBSScheduler, SlurmScheduler, LSFScheduler.

Move from utils.py → core/batch/

• batch_jobid, get_batch_script_for_job, get_project,
  get_charge_account, add_mail_type_args, resolve_mail_type_args,
  transform_vars.

Move from utils.py → core/shell.py

• run_cmd, run_cmd_no_fail (general utility, pulled here because batch
  is the first heavy consumer).

Consolidation

• transform_vars (utils.py:2118) takes case and calls
  case.get_value() repeatedly — consolidate as a Case method, with
  core template logic in CIME/core/batch/.
• batch_jobid (utils.py:2360) calls case.get_job_id() — move into
  the batch subsystem.

Imports & re-exports

• Update internal CIME imports to point at core/batch/.
• Leave re-exports in utils.py, case/case_submit.py for external
  consumers.

Definition of done

• All batch tests pass.
• External models (E3SM, CESM, NorESM) submit jobs unchanged.
• Batch logic lives in core/batch/, not in XML/, case/, utils.py.
• EnvBatch is a thin wrapper.
• Scheduler protocol with PBS/Slurm/LSF implementations.
• 80%+ coverage on core/batch/.

Related

• Depends on Refactor Slice 1: Foundation (typed exceptions, bootstrap, kill star imports) #4996 (foundation, exception hierarchy)
• Blocks Refactor Slice 3B: Move build logic into CIME/core/build/ #4999 (build orchestration may depend on batch interface)