Cleanups & reorginization for 0.6.0 release

[dmjoy]

• Remove old and unused code (thinking everything that's no longer used as of the Phase 1 final evaluation can probably go) -- More detailed issue: Code cleanup specifics (for 0.6.0) #232
• Organize align_system/algorithms into align_system/algorithms/adms and align_system/algorithms/adm_components
• Make a pass over documentation (making sure it's still up to date) and update this table (woefully out of date): https://github.com/ITM-Kitware/align-system?tab=readme-ov-file#system-requirements-by-algorithm--model
• (Maybe) break apart and organize align_system/prompt_engineering/outlines_prompts.py