Refactor Real Life Challenges simulator

[j-atkins]

Summary of Changes

This PR refactors the problems/Real Life Challenges simulation module, execution loop, and checkpoint verification logic. Primary objectives are:

• Decouple problem tracking from temporary JSON log files by utilizing ScheduledProblem and ActiveProblem objects as the single source of truth for problem states and resolution.
• Unify execution, problem loading/selection, reporting, and expedition uniqueness checks directly into ProblemSimulator class rather than spreading the logic across _run.py.
• Also move Checkpoint verification checks, whereas before there was too much problems module associated logic handled by Checkpoint.
• Account for Port waypoints (see Timedeltas and arrival/departure ports from MFP export #372) when communicating waypoint numbers to the user via a new helper utility _get_public_wp()
• Refactor_run.py: more helper functions, clean up.

Detailed Changes

problems/simulator.py

• New ScheduledProblem dataclass (pairs a problem with its waypoint index and resolution state) and SelectedProblems dataclass as a container for managing problem states and iteration through problems.
• Move/new execute_for_instrument(), verify_problem_resolution(), and create_post_expedition_report() methods directly to ProblemSimulator.
• Updated problem logging, checkpoint handling, and report generation to map raw waypoint indices to public numbers using _get_public_wp().
• Removed writing and reading separate problem_<hash>.json files per problem occurrence. Replaced with structured caching of SelectedProblems in the ProblemSimulator.

_run.py

• Refactored _run() function by extracting steps into helper methods.
• Moved problem initialisation/resolution checks entirely to ProblemSimulator.

checkpoint.py

• Introduced ActiveProblem to track runtime problem states (delay duration, problem waypoint index, and resolution status).
• Refactored Checkpoint.verify() into verify_past_schedule(), focusing solely on ensuring past waypoints are untouched and decoupling from problems logic.

expedition.py & utils.py

• New _get_public_wp() in utils.py to translate raw/internal schedules into user-facing waypoint numbers. Helps ensure consistency and over-reliance on plus-one indexing in all cases.
• Updated schedule validation error messages in expedition.py to use public waypoint numbers correctly.

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Closes #283, closes #303