v1.11.0: journal-style figures and tables (condensed Fig. 5, Fig. S1 audits, graphical abstract)

Release cited by the manuscript revised to Molecular Neurodegeneration author guidelines and house style. No analysis results changed; this release covers figures, tables and their wording.

Figures

• Fig. 5 (single-nucleus design effects) now has four panels for the ALS-up module only: Pineda processing date, Ulm age, Li depth, and the ALS-up forest plot (fig4_meta.R adds pa_up).
• Supplementary Fig. S1 is now "cohort-design audits". It keeps the discovery audit (a-d) and gains the panels moved out of Fig. 5: processing-date variance (e), the cross-cohort replication matrix (f) and the two-module forest plot (g).
• Fig. 4d has an Interpretation box.
• Graphical abstract. compose_figures_v3.R writes results/Figures_v3/Graphical_abstract/graphical_abstract.png (920 × 300 px).
• Labels. Panel labels are reworded throughout: "ALS-up module", "consensus up genes", "fixed modules", and "Analysis plan" in the Fig. 1 legend key.

Supplementary Tables

• In reader-facing text in S1-S3 and the README sheet, "Amendment N" now reads "analysis document N". Repository file paths keep their names, so the SHA-256 values in S1 still match docs/analysis_plans/.
• S1 is renamed Supplementary_Table_S1_analysis_plan_documents.tsv.