Add arbitrary fixed-effect contrasts

README.md

@@ -27,6 +27,8 @@ The engine diagonalizes the GRM once, rotates the common design and every unique
 - Variable numbers of extra fixed-effect covariates per task through a CSR index.
 - Satterthwaite t/F fixed-effect inference by default, with optional
   Kenward-Roger F tests and a joint test of task-specific covariates.
+- Named arbitrary linear contrasts over the common fixed-effect design, using
+  the Satterthwaite or Kenward-Roger method selected for the run.
 - Atomic block output and safe resume/force semantics.
 - Generic Python CLI for manifest creation, validation, execution, provenance signatures, status, and result export.
 
@@ -114,11 +116,14 @@ python python/spectra_reml.py make-manifest \
   --tasks data/tasks.tsv \
   --extra-offsets data/extra_offsets.i64.bin \
   --extra-indices data/extra_indices.i32.bin \
+  --contrast-matrix data/contrasts.f64.bin \
+  --contrast-metadata data/contrasts.tsv \
   --output-dir work/blocks \
   --n-samples 3523 \
   --n-base-covariates 8 \
   --n-phenotype-rows 10000 \
-  --n-extra-covariate-rows 2000
+  --n-extra-covariate-rows 2000 \
+  --n-contrasts 5
 ```
 
 Validate, run, and export results:
@@ -141,6 +146,14 @@ python python/spectra_reml.py finalize \
 
 `results.tsv.gz` retains the complete per-task summary and stores the fixed-effect vector and row-wise packed lower covariance as JSON arrays.
 
+Optional named contrasts are supplied by `--contrast-matrix`,
+`--contrast-metadata`, and `--n-contrasts`. Contrast rows act on `base_x`;
+task-specific covariate columns receive zero weights automatically. Finalized
+results contain contrast estimates, adjusted standard errors, statistics,
+numerator and denominator degrees of freedom, and p-values as JSON arrays.
+This release uses manifest v2, run-signature v2, block v3, and finalized-output
+v2 contracts. It intentionally does not read older contracts.
+
 Fixed-effect inference defaults to Satterthwaite. Select Kenward-Roger or turn
 inference off with `--fixed-effect-test kenward-roger` or
 `--fixed-effect-test none`. Coefficient-wise standard errors, statistics,