Merge branch 'phase2-secondary-prediction' into 4-prototype-a-mixture-of-experts-routing-tree-architecture

Brings in the rollout-validation fixes developed alongside Phase 2
(exact e_sec budget rescaling in decode_secondaries, filtering
synthetic termination rows out of load_rollout_vs_truth, Tier 4 truth
overlay, --energy-gev support in dwarf make-root) and reconciles them
with this branch's mixture-of-experts routing work: build_features/
build_models/dataset plumbing keep the ProcessRouter's proc_map/
proc_idx threading, and create_root_files.py's job_seed folds in both
the per-job seed derivation and the new energy_gev component.

tests/test_transforms.py

@@ -263,6 +263,14 @@ def _minimal_step_data(N: int, process: np.ndarray | None = None) -> dict:
     return data
 
 
+def _step_data_no_sec_lists(n_sec: np.ndarray) -> dict:
+    """Minimal build_features input with n_sec but no per-secondary list columns
+    (mimics a parquet that skipped the parent->child join)."""
+    data = _minimal_step_data(len(n_sec))
+    data["n_sec"] = np.asarray(n_sec, dtype=np.int32)
+    return data
+
+
 def test_build_features_proc_idx_zero_without_proc_map():
     data = _minimal_step_data(3, process=np.array(["compt", "phot", "eIoni"], dtype=object))
     pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
@@ -287,8 +295,7 @@ def test_build_features_require_secondaries_raises_when_lists_missing():
     through the parent->child join; require_secondaries must catch it instead of
     silently zeroing every Stage-2 target (regression: this collapsed the
     secondary species to a single PDG index during training)."""
-    data = _minimal_step_data(3)
-    data["n_sec"] = np.array([0, 2, 1], dtype=np.int32)  # secondaries, but no lists
+    data = _step_data_no_sec_lists(np.array([0, 2, 1]))
     pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
 
     with pytest.raises(ValueError, match="per-secondary columns"):
@@ -298,7 +305,7 @@ def test_build_features_require_secondaries_raises_when_lists_missing():
 def test_build_features_require_secondaries_ok_when_no_secondaries():
     """require_secondaries only fires when secondaries actually exist; a file
     with n_sec == 0 everywhere (e.g. Stage-1-only) must still load."""
-    data = _minimal_step_data(3)  # n_sec all zero
+    data = _step_data_no_sec_lists(np.zeros(3, dtype=np.int32))
     pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
 
     _, _, _, _, sec_cont, sec_pdg_idx, *_ = build_features(