v0.3.0 post-implementation audit: resolve all 9 tracked discrepancies

Works through docs/v0.3.0-followups.md item by item, closing the gap
between the design doc and the shipped v0.3.0-stage2-autoregressive code:

1. validate.py: 7-tuple batch unpacking, sample_stage1/sample_stage2
   dispatch, stage-2 particle-type-class marginal.
2. Stage-prefixed --stage1-*/--stage2-* CLI flags for train/new-run.
3. Thread stage2_model.k_max through loader/transforms/dataset/pipeline/
   train instead of the hardcoded K_MAX constant.
4. Mixed conditioning.particle.type / conditioning.material.type support
   end-to-end (data pipeline + dwarf warm-cache).
5. conditioning.share_stages = true: one shared ConditionEncoder instance
   across both stages.
6. stage2_model.generator = "ddpm" formally deferred into design doc §11.2
   (was silently unimplemented).
7. giant predict/rollout: implement conditioning.*.type = "onehot" via the
   checkpoint's saved pdg_topn_map/mat_topn_map.
8. network.py's checkpoint-path model_config migration now fails loudly on
   non-zero legacy expert_hidden_dim/expert_n_blocks, matching config.py's
   TOML-load path (§4.2).
9. validate_config now rejects stage2_model.n_sec.mode = "truth" for a
   rollout-capable checkpoint (§9).

Also cleared all pre-existing `ty check` noise (44 -> 0 diagnostics),
mostly a test-helper dict-unpack pattern that made every unrelated
constructor keyword look like a type error.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

tests/test_config.py

@@ -584,21 +584,19 @@ def test_validate_config_embedding_target_passes_with_embedding_conditioning():
     gconfig.validate_config(cfg)  # must not raise
 
 
-def test_validate_config_mixed_particle_material_conditioning_not_supported():
-    """The data pipeline doesn't support mixed conditioning types yet, even
-    though ConditionEncoder itself already can (docs/v0.3.0-design.md §3.1
-    vs. giant/data/transforms.py's still-single conditioning param)."""
+def test_validate_config_mixed_particle_material_conditioning_is_valid():
+    """docs/v0.3.0-design.md §3.1: the particle and material conditioning
+    axes are configured independently and may mix freely — e.g. material
+    "physical" with particle "embedding" — and the data pipeline
+    (giant/data/transforms.py) now implements that end-to-end, so
+    validate_config must not reject it."""
     cfg = _cfg_with(
         **{
             "conditioning.particle.type": "physical",
             "conditioning.material.type": "embedding",
         }
     )
-    try:
-        gconfig.validate_config(cfg)
-        assert False, "expected ValueError"
-    except ValueError as e:
-        assert "mixed" in str(e) or "conditioning.material.type" in str(e)
+    gconfig.validate_config(cfg)  # must not raise
 
 
 def test_validate_config_pdg_router_incompatible_with_physical_conditioning():
@@ -639,6 +637,49 @@ def test_validate_config_stop_token_not_implemented():
         assert "stop_token" in str(e)
 
 
+def test_validate_config_n_sec_truth_rejected_for_rollout_capable_checkpoint():
+    """docs/v0.3.0-design.md §9: 'n_sec.mode = "truth" is invalid for a
+    rollout-capable checkpoint' — both stages active means giant rollout
+    could load this checkpoint, but 'truth' has no ground truth to draw
+    n_sec from at rollout time."""
+    cfg = _cfg_with(
+        **{
+            "stage2_model.n_sec.mode": "truth",
+            "stage1_model.active": True,
+            "stage2_model.active": True,
+        }
+    )
+    try:
+        gconfig.validate_config(cfg)
+        assert False, "expected ValueError"
+    except ValueError as e:
+        assert "n_sec.mode" in str(e) and "truth" in str(e)
+
+
+def test_validate_config_n_sec_truth_allowed_for_stage2_only_checkpoint():
+    """'truth' is exactly the standalone stage-2 evaluation mode the design
+    doc carves out — stage1_model.active = false must still pass."""
+    cfg = _cfg_with(
+        **{
+            "stage2_model.n_sec.mode": "truth",
+            "stage1_model.active": False,
+            "stage2_model.active": True,
+        }
+    )
+    gconfig.validate_config(cfg)  # must not raise
+
+
+def test_validate_config_n_sec_truth_allowed_when_stage2_inactive():
+    cfg = _cfg_with(
+        **{
+            "stage2_model.n_sec.mode": "truth",
+            "stage1_model.active": True,
+            "stage2_model.active": False,
+        }
+    )
+    gconfig.validate_config(cfg)  # must not raise
+
+
 def test_validate_config_ar_default_markov_always_passes():
     """DEFAULT_CONFIG already has decoder='autoregressive',
     history='markov', teacher_forcing='always' — must not raise (v0.3.0