path,kind,description,status,expected_local_path,checkpoint_role
src/paper_ai_diffraction/core/model.py,source,Core model definition,copied,,
src/paper_ai_diffraction/core/dataset.py,source,Dataset loading including mixed dual-source support,copied,,
src/paper_ai_diffraction/core/train.py,source,Training entrypoint,copied,,
src/paper_ai_diffraction/core/inference.py,source,Inference helpers,copied,,
src/paper_ai_diffraction/core/streaming_dataset.py,source,Streaming dataset helper retained because train.py imports it,copied,,
src/paper_ai_diffraction/utils/extinction_multilabel.py,source,Extinction-group multilabel utilities,copied,,
src/paper_ai_diffraction/eval/evaluate_calibration_metrics.py,source,Calibration metrics evaluation,copied,,
src/paper_ai_diffraction/eval/evaluate_split_head_validity.py,source,Split-head validity evaluation,copied,,
src/paper_ai_diffraction/topology/compare_325_failure_modes.py,source,Topology/failure-mode comparison,copied,,
src/paper_ai_diffraction/topology/plot_extinction_topology_flow.py,source,Topology-flow figure generation,copied,,
src/paper_ai_diffraction/topology/analyze_topological_error_distance.py,source,Topology distance summary analysis,copied,,
src/paper_ai_diffraction/topology/plot_topological_error_distance.py,source,Topology distance plotting,copied,,
src/paper_ai_diffraction/eval/plot_calibration_sweep.py,source,Calibration sweep plotting,copied,,
assets/figure_data/stage2c_r325_temp_sweep.json,asset,Compact Stage-2c temperature sweep used for the calibration figure,copied,,
assets/figure_data/physics_pe_curve_82ept35h.json,asset,Compact checkpoint curve used for the physics-PE supplementary figure,copied,,
configs/final_mixed_2500k_dualsource.json,config,Sanitized final champion evaluation config,copied,,
scripts/eval_rruff_325_473.sh,script,Paper-facing benchmark evaluation wrapper,authored,,
scripts/make_topology_flow_figure.sh,script,Paper-facing topology-flow wrapper,authored,,
scripts/make_topology_distance_figure.sh,script,Paper-facing topology-distance wrapper,authored,,
scripts/make_calibration_figure.sh,script,Paper-facing calibration sweep wrapper,authored,,
scripts/make_curriculum_real_holdout.py,script,Paper-facing Figure 2 generator from bundled benchmark values,adapted,,
scripts/make_stage_decoder_tradeoffs_rruff473.py,script,Paper-facing Figure 3 generator from bundled benchmark values,adapted,,
scripts/make_physics_pe_q2_ruler.py,script,Paper-facing S8 generator from bundled checkpoint-curve JSON,authored,,
scripts/reconstruct_rruff_473.py,script,Public algorithm for reconstructing the frozen RRUFF-473 benchmark from upstream manifest and XY data,adapted,,
scripts/build_rruff_325_from_473.py,script,Public deterministic builder for RRUFF-325 from frozen RRUFF-473,adapted,,
scripts/make_main_tables.py,script,Paper-facing table-generation script,authored,,
results/,directory,Compact JSON outputs used in paper; generated figures are intentionally excluded from git,copied,,
docs/TRAINING.md,doc,Paper-facing training instructions,authored,,
docs/EVALUATION.md,doc,Paper-facing evaluation instructions,authored,,
docs/FIGURES.md,doc,Paper-facing figure instructions,authored,,
docs/BENCHMARKS.md,doc,Benchmark-construction and non-redistribution notes for RRUFF-473 and RRUFF-325,authored,,
assets/topology/extinction_group_adjacency.json,asset,Condensed extinction-group topology graph,copied,,
reproducibility/checkpoint_manifest.csv,metadata,Checkpoint linkage manifest,generated,,
reproducibility/dataset_manifest.csv,metadata,Dataset and external-asset manifest,generated,,
results/reviewer/ext_group_priors.json,asset,Compact aggregate extinction-group prior for calibration; rounded probabilities/log-priors and seen-class flags only; no raw ICSD structures or per-structure records,authored,,
results/reviewer/ext_group_priors.csv,asset,CSV form of compact aggregate extinction-group prior for calibration,authored,,
results/reviewer/rruff325_precomputed_inference.json,asset,Compact precomputed RRUFF-325 inference summary for reviewer inspection,authored,,
metadata/croissant_rai.jsonld,metadata,Self-contained Croissant JSON-LD file with core file metadata and minimal Responsible AI fields for the dataset release,authored,,