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>

scripts/bump_dataset_version.py

@@ -472,14 +472,17 @@ def plan_update_manifest(
                 parts[schema_idx] = new_schema
                 changed = True
 
-        if not changed:
-            result.append((raw, None))
-            continue
-
+        # Check existence for every data line, not just ones whose gen/schema
+        # actually changed — an already-correct-looking line can still point
+        # at a file that was deleted or moved out-of-band.
         new_abs = Path(*parts)
         if not new_abs.exists():
             missing.append(new_abs)
 
+        if not changed:
+            result.append((raw, None))
+            continue
+
         new_rel = os.path.relpath(new_abs, start=manifest_dir)
         result.append((raw, new_rel))