Fix silent failure modes surfaced by extensive code review

- energy_simplex_encode: warn when clipping post_E to pre_E discards
  recorded edep/e_sec instead of silently zeroing them
- local/inv_local_frame_rotation: validate and normalize pre_dir instead
  of silently assuming unit norm; raise on near-zero-norm rows
- train(): make --lr authoritative on resume instead of being silently
  overwritten by the checkpoint's optimizer/scheduler state; print and
  exit cleanly instead of silently training zero epochs when the
  checkpoint already meets --epochs; truncate metrics.csv on a fresh
  run instead of always appending
- dwarf update-manifest: check file existence for every manifest line,
  not just ones whose gen/schema actually changed
- pyproject.toml: dev extra now pulls in convert+analysis so the
  documented `uv sync --extra cpu --extra dev` + `pytest` actually
  passes collection

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

tests/test_transforms.py

@@ -1,7 +1,9 @@
 import numpy as np
+import pytest
 from giant.data.transforms import (
     energy_simplex_decode,
     energy_simplex_encode,
+    inv_local_frame_rotation,
     inv_log_transform,
     local_frame_rotation,
     log_transform,
@@ -53,6 +55,35 @@ def test_local_frame_rotation_preserves_norm():
     np.testing.assert_allclose(np.linalg.norm(result, axis=1), 1.0, atol=1e-5)
 
 
+def test_local_frame_rotation_rejects_near_zero_pre_dir():
+    """A degenerate (near-zero-norm) pre_dir has no well-defined frame — must
+    raise instead of silently falling back to an arbitrary rotation axis."""
+    pre_dir = np.array([[0.0, 0.0, 0.0], [0.0, 0.0, 1.0]], dtype=np.float32)
+    post_dir = np.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], dtype=np.float32)
+    with pytest.raises(ValueError, match="near-zero norm"):
+        local_frame_rotation(pre_dir, post_dir)
+    with pytest.raises(ValueError, match="near-zero norm"):
+        inv_local_frame_rotation(pre_dir, post_dir)
+
+
+def test_local_frame_rotation_normalizes_non_unit_pre_dir():
+    """A pre_dir with float32-drift norm (not exactly 1) must still produce the
+    same result as its exactly-normalized counterpart, not a skewed frame."""
+    rng = np.random.default_rng(9)
+    N = 50
+    pre_dir_unit = rng.standard_normal((N, 3)).astype(np.float32)
+    pre_dir_unit /= np.linalg.norm(pre_dir_unit, axis=1, keepdims=True)
+    post_dir = rng.standard_normal((N, 3)).astype(np.float32)
+    post_dir /= np.linalg.norm(post_dir, axis=1, keepdims=True)
+
+    pre_dir_scaled = pre_dir_unit * rng.uniform(0.9, 1.1, size=(N, 1)).astype(
+        np.float32
+    )
+    expected = local_frame_rotation(pre_dir_unit, post_dir)
+    result = local_frame_rotation(pre_dir_scaled, post_dir)
+    np.testing.assert_allclose(result, expected, atol=1e-4)
+
+
 def test_travel_direction_is_unit_norm():
     rng = np.random.default_rng(5)
     N = 50