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>

uv.lock

@@ -464,14 +464,20 @@ cuda = [
     { name = "torch", version = "2.3.1+cu118", source = { registry = "https://download.pytorch.org/whl/cu118" } },
 ]
 dev = [
+    { name = "awkward" },
+    { name = "ipykernel" },
+    { name = "matplotlib" },
+    { name = "polars" },
     { name = "pytest" },
     { name = "ruff" },
     { name = "ty" },
+    { name = "uproot" },
 ]
 
 [package.metadata]
 requires-dist = [
     { name = "awkward", marker = "extra == 'convert'", specifier = ">=2.6,<3" },
+    { name = "giant", extras = ["convert", "analysis"], marker = "extra == 'dev'" },
     { name = "ipykernel", marker = "extra == 'analysis'", specifier = ">=7.3.0" },
     { name = "matplotlib", marker = "extra == 'analysis'", specifier = ">=3.8,<4" },
     { name = "numpy", specifier = ">=1.26,<3" },