docs: fix the verification step and ship the homophily tail metrics

Move analysis and pipeline code to the code repository; keep the model, its loader, the data and the docs

Remove hardcoded paths from src_at_ef0b17d.tar

Remove hardcoded paths from src_at_9d74e93.tar

Replace hardcoded paths with placeholders: pooled_edge_homophily.json

Replace hardcoded paths with placeholders: compute_pooled_edge_homophily.py

Replace hardcoded paths with placeholders: run_cellvit_pipeline.sh

Replace hardcoded paths with placeholders: fat_tail_followup.py

Replace hardcoded paths with placeholders: run_fullregen.sh

Replace hardcoded paths with placeholders: nucls_super_source_args.json

Replace hardcoded paths with placeholders: run_optuna_repro.sh

Replace hardcoded paths with placeholders: commands.txt

Remove internal reproduction notes; their content is now in DATA.md

Restructure: move batch 10/30

Restructure: move batch 9/30