Convert setPheno and crossing functions to S4 generics; add Pop/MultiPop methods, centralize internals, and update docs

[mghaderizefreh]

Summary

• Refactors key APIs to S4 generics to enable method dispatch and easier extension to new classes.
• No intended changes to user-facing behavior for existing Pop workflows.

Key changes

• setPheno
  • Converted to an S4 generic
    (setGeneric("setPheno", ...)).
  • Added methods for Pop and MultiPop (is this needed?).
  • Extracted shared implementation into
    .setPheno_internal().
  • Exported method in NAMESPACE and updated Rd with method aliases and usage.
• Crossing API (R/crossing.R)
  • Converted the following to S4 generics with Pop methods and shared internal implementations:
    • makeCross → .makeCross_internal
    • makeCross2 → .makeCross2_internal
      (methods for females = Pop, males = Pop)
    • randCross → .randCross_internal
    • randCross2 → .randCross2_internal
      (methods for females = Pop, males = Pop)
    • selectCross → .selectCross_internal
    • self → .self_internal
    • makeDH → .makeDH_internal
• Minor spelling fixes in error messages and docs:
• sortPed error now references “maxCycle” consistently.