feat(cli): separate-branches rename, short aliases, clean dry-run

- --normalize-to-one renamed to --separate-branches (no alias; the
  name now describes the output choice: total spectrum with
  intensity-normalized branches vs separate branches, each
  normalized to unit area with intensities left to the data user).
  SpectrumConfig.normalize_to_one -> separate_branches, CSV header
  word to_one -> separate.
- every long option gains a single-letter alias: -N -i -s -m -o -p
  -L -d -c -V -S -b (only -v/-q existed before)
- dry-run drops the top-level Transition: line — the per-branch
  list below already reports each branch's transition type
- version bumped to 0.4.1 (pyproject, __version__, CSV semantics
  docstring, TODO roadmap entry)

TODO.md

@@ -322,7 +322,7 @@ ______________________________________________________________________
 
 ## Current Status
 
-**Version:** 0.3.1 → **In progress: 0.4.0 — Package restructuring**
+**Version:** 0.4.0 → **v0.4.1 — CLI options refresh & normalization fixes** (released on `dev/core-fermi-csv`)
 
 ### Completed (v0.3.x)
 
@@ -354,6 +354,12 @@ ______________________________________________________________________
   - README updated with new architecture diagram and Quick Start examples
   - Version bumped to 0.4.0
 
+### Completed (v0.4.1)
+
+- Core spectrum made unconditional (`phase_space × fermi`): core toggles removed, physical branch spectra in CSV export, plots built from the exported CSV
+- Normalization audit fixes: lone surviving branch defines the spectrum, CLI options propagate through the JSON flow, positive-integral guard for both export modes, paceENSDF per-branch measured endpoints (Co60 fixed), single delegated paceENSDF config builder
+- CLI surface refresh: `--normalize-to-one` renamed to `--separate-branches` (no alias), single-letter aliases for every option, dry-run drops the redundant top-level `Transition:` line, stale detector_* JSON schema keys removed
+
 ### Next Immediate Step
 
 - **Track A: ⁹⁹Tc spectrum-shape analysis** — start real data processing pipeline