Track the documented Slurm wrappers that an unanchored slurm/ ignore rule
excluded, move graph-cache preparation from config.application into
graphs.preparation (outputs verified identical to main), archive rewrite
task specs under docs/history, move the paper source under docs/paper,
remove empty scaffolding, and refresh stale transformer documentation.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
