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Document explicit f3 checkpoint directories
Document all cell-line expression checkpoints
Document f1 and f2 expression checkpoints
Document gene-expression checkpoints
Remove deleted visualization notebook references
Clarify supported raw-data workflows
Document automatic average Hi-C fallback
Clarify reproducible HPC workflow
Wiki: pipeline naming (drop reproduction); update branch + HF repo references
Initialize wiki: overview, setup, datasets, Part 1/2, other cells, notebooks, troubleshooting