feat(cli): add port flags for start/restart and warn on misuse

[kamran-rapidfireAI]

• Add --port (-p), --mlflow-port, and --api-port CLI flags
• Apply only to start and restart; validate ports (1–65535)
• Map flags to env vars RF_FRONTEND_PORT, RF_MLFLOW_PORT, RF_API_PORT
• Update script runner to support env overrides
• Print a warning if port flags are passed to non-applicable commands (e.g., init, status)
• Defaults remain unchanged (frontend 3000, MLflow 5002, API 8080)

Examples:

• rapidfireai start --port 4000
• rapidfireai start --mlflow-port 6000 --api-port 9090
• rapidfireai restart -p 4000

Changes

• Brief description of the changes in this PR. Include breaking changes or any unusual behavior.

Testing

• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
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• I have added tests that prove my fix is effective or that my feature works
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Performance Impact

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Related Issues

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