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_9d74e93.tar

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