- Updated output paths in various command files to reflect the new structure: `.workflow/sessions/{session_id}/` instead of `.workflow/{session_id}/`.
- Adjusted documentation and code comments to ensure consistency across all agents and commands.
- Ensured that all references to session-related files are correctly pointing to the new directory format.
- Updated references in various workflow commands to utilize role analysis documents instead of synthesis-specification.md.
- Modified CLI templates and command references to reflect the new architecture and document structure.
- Introduced conflict-resolution command to analyze and resolve conflicts between implementation plans and existing codebase.
- Deprecated synthesis role template and provided migration guidance for transitioning to the new role analysis approach.
