v1.10.0: within-lineage source test (Amendment 16) and single-module figure set

Release cited by the simplified manuscript, which follows one signature (the frozen ALS-up module): bulk replication, ventral-horn localisation, a myeloid-led multicellular state, and the single-nucleus design lesson.

New

• Amendment 16 and W74 (scripts/run_w74_within_lineage_source.R, docs/analyses/W74_within_lineage_source.md): a within-lineage test of whether the ALS-up signal is shared with the microglial compartment. The discovery microglial compartment showed a small same-direction shift, mainly GPNMB (fry P = 0.021, median log2FC 0.17, against 2.33 in astrocytes). The astrocyte-minus-microglia interaction was larger in astrocytes in Zelic and not distinguishable in Ulm and Pineda BA9 (combined signed z = 1.84, P = 0.066). The prespecified overall reading is mixed, and the result is not used in the manuscript conclusions. It is listed in Supplementary Tables S1 and S2.

Changed

• Figures: Fig. 2 now shows the frozen-module tests (a) and gene-level fold changes (b). The consensus-signature panels moved to Supplementary Fig. S3a,b, and the clinical association to S3c. Fig. 3a shows the ALS-up module only. Fig. 1a no longer lists the consensus signature.
• compose_figures_v3.R: fixed source-data directory names (Fig. 2 and Fig. 5 source data were previously not copied). Each figure now receives only the source data of its own panels.
• Supplementary Tables S1 (Amendment 16) and S2 (one W74 row).