docs: drop em dashes from the markdown

Fix stale paths and resync the shipped modeling code

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

Remove a non-runnable duplicate survival script (PATH/TO placeholders)

Replace hardcoded paths with placeholders: rebase_graph_paths.py

Ship the parameterized survival scripts (no hardcoded paths, CLI args)

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

Restructure: move batch 30/30

Restructure: move batch 10/30

Restructure: move batch 1/1