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>

pyproject.toml

@@ -24,6 +24,7 @@ dev = [
     "pytest>=8,<10",
     "ruff>=0.15,<1",
     "ty>=0.0.50,<0.1",
+    "giant[convert,analysis]",
 ]
 convert = [
     "uproot>=5.3,<6",