Plan integration roadmap for nascent RNA pipeline enhancements

## Summary Create a comprehensive roadmap for integrating features from PEPPRO, NRSA/eNRSA, BidirectionalFlow, and MuMerge. ## Tasks - [ ] Prioritize feature implementation order - [ ] Design module architecture for new features - [ ] Plan testing strategy for each enhancement - [ ] Create compatibility matrix with existing features - [ ] Design configuration schema updates ## Dependencies This issue tracks the overall integration strategy for issues #1-12. ## Acceptance criteria - [ ] Clear implementation timeline - [ ] Module architecture documentation - [ ] Testing strategy defined - [ ] Configuration updates planned