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refactor: cleanup repo, add SLURM scripts, document reproducibility
Major cleanup and improvements for the CPR repository: ## Cleanup - Remove duplicate notebooks from root dirs (afdb/, scope/, clean_selection/) These are archived in notebooks_archive/ (now gitignored) Organized versions remain in notebooks/ - Delete legacy dockerfile (keep modern Dockerfile with PyTorch base) - Remove large binary files from git tracking (84MB+ .npy, .pkl files) - Update .gitignore for build artifacts, caches, model files ## New Features - Add SLURM scripts for HPC workflows: - slurm_build_apptainer.sh: Build container on compute node - slurm_compute_fdr_thresholds.sh: Compute FDR threshold lookup table - Add compute_fdr_table.py: Generate FDR thresholds at standard alpha levels - Add docs/REPRODUCIBILITY.md: Document expected variability in results ## Documentation Updates (CLAUDE.md) - Add $HOME2 storage instructions (avoid disk quota on $HOME) - Add SLURM requirement for GPU/CPU-intensive tasks - Document available partitions (standard, gpu, memory) ## …f7a768a
