refactor: refine CLI options and enhance debug logging

- Remove --mode, --transition-type, and --decay-index CLI flags
  (parameters now come from ENSDF data or custom JSON input)
- Clarify energy units in all CLI help text (MeV throughout, keV for detector params)
- Enhance logging verbosity:
  - -v (INFO): shows source, component initialization, workflow steps
  - -vv (DEBUG): shows detailed internals of all spectrum components
    (parameters, evaluation counts, input/output ranges)
- Improve CSV headers with element notation (e.g. Tc99 -> Ru99)
- Add CONVENTIONS.md documenting energy unit and logging conventions
- Update TODO.md with completion status

scripts/run_notebooks.py

@@ -98,7 +98,9 @@ def main():
                     failed.append(nb.name)
 
     print()
-    print(f"Done. {len(all_plots)} plot(s) extracted, {len(failed)} notebook(s) failed.")
+    print(
+        f"Done. {len(all_plots)} plot(s) extracted, {len(failed)} notebook(s) failed."
+    )
     if all_plots:
         print()
         print("Plots saved to: notebooks/_plots/")