refactor: make extra field appending independent of replacement logic

[berntpopp]

Currently, our logic for appending extra sample fields (DP, AD, etc.) is tightly coupled with genotype replacement. We want to decouple or modularize this so that extra fields can be appended even if genotype replacement is turned off (or vice versa).

Details & Acceptance Criteria

• Separate the “append extra sample fields” steps into a self-contained function/module, ensuring it can be called independently from the main genotype replacement flow.
• Preserve existing functionality (no regressions): if a user still wants genotype replacement + extra fields, it should remain seamless.
• Document the new approach so users can enable/disable them individually.

Why This Is Valuable

• Improves code maintainability by separating concerns.
• Offers more configuration flexibility for users who only need one feature without the other.