docs: update documentation files and fix linting issues

TODO.md

@@ -51,8 +51,11 @@ fitter/                     ← main analysis framework
 ├── result.py               ← FitResult, analysis results
 # └── report.py               ← PDF report generation (deferred)
 
-visualize/                  ← visualization / plotting
-└── visualize/__init__.py   ← BetaSpectrumAnalyzer
+output/                     ← output, visualization, CSV export
+├── __init__.py             ← BetaSpectrumAnalyzer, CSVEmitter, Visualizer
+├── core.py                 ← BetaSpectrumAnalyzer base class
+├── csv_export.py           ← CSV export functionality
+└── visualization.py        ← Plotting and visualization functionality
 ```
 
 ### Rationale
@@ -64,6 +67,7 @@ visualize/                  ← visualization / plotting
 ### Migration Plan
 
 #### Phase 1: Create `exp_data` module ✅ COMPLETE
+
 - [x] `exp_data/spectrum.py` — `ExpSpectrum` dataclass: energies, counts, errors, metadata
 - [x] `exp_data/calibration.py` — `EnergyCalibrator` + `CalibrationResult`: linear/quadratic channel→energy
 - [x] `exp_data/fitters.py` — `GaussianFitter` + `PeakFitter`: peak detection and fitting
@@ -71,6 +75,7 @@ visualize/                  ← visualization / plotting
 - [x] 43 tests, ruff + mypy clean
 
 #### Phase 2: Create `fitter` module ✅ COMPLETE
+
 - [x] `fitter/model.py` — `SpectrumModel`: wraps `BetaSpectrum` + `DetectorResponse`, callable model with convolution
 - [x] `fitter/fit_engine.py` — `SpectrumFitter` + `FitConfig` + `FitResult`: χ² fitting, covariance, profile likelihood, confidence intervals
 - [x] `fitter/extractor.py` — `CWExtractor` + `GVAExtractor`: C(W) and g_V/g_A extraction
@@ -79,6 +84,7 @@ visualize/                  ← visualization / plotting
 - [x] Detector convolution handles W < 1.0 edge cases
 
 #### Phase 3: Clean up `beta_spectrum` ✅ COMPLETE
+
 - [x] Remove `cw_extractor.py` (moved to `fitter/extractor.py`)
 - [x] Remove `fitter.py` (moved to `fitter/fit_engine.py`)
 - [x] Clean up `__init__.py` — only exports theory classes
@@ -88,6 +94,7 @@ visualize/                  ← visualization / plotting
 - [x] 322 tests pass, ruff + mypy clean on all 26 source files
 
 #### Phase 4: Update package structure ✅ COMPLETE
+
 - [x] `pyproject.toml` auto-discovers all 4 packages via `setuptools.packages.find`
 - [x] `beta_spectrum.cli` keeps CLI entry point (no re-exports needed)
 - [x] All imports updated across 26 source files
@@ -313,6 +320,7 @@ ______________________________________________________________________
 **Version:** 0.3.1 → **In progress: 0.4.0 — Package restructuring**
 
 ### Completed (v0.3.x)
+
 - All theoretical corrections: phase space, Fermi function, finite size, screening, exchange, radiative (with delta_cut resummation)
 - Detector response module with analytical models (Gaussian, Gaussian+tail, Tikhonov), convolution API
 - χ² curve fitting framework (CurveFitter) with confidence intervals, profile likelihood, correlation analysis
@@ -327,20 +335,22 @@ ______________________________________________________________________
 - Plot output: unified multi-branch approach, externalized headers, compact legends, consistent titles
 
 ### Completed (v0.4.0)
+
 - **Track B: Package restructuring** — separating into `beta_spectrum` (theory), `exp_data` (experimental data), `fitter` (analysis framework)
   - [x] Phase 1: Create `exp_data` module (raw_data.py, calibration.py, fitters.py, corrections.py, spectrum.py) — 43 tests
   - [x] Phase 2: Create `fitter` module (model.py, fit_engine.py, extractor.py, result.py) — 34 tests
-  - [x] Phase 3: Clean up `beta_spectrum` (remove cw_extractor.py, fitter.py, __init__.py cleanup) — 322 tests
+  - [x] Phase 3: Clean up `beta_spectrum` (remove cw_extractor.py, fitter.py, **init**.py cleanup) — 322 tests
   - [x] Phase 4: Package auto-discovered by setuptools, all imports updated, black formatting applied
 - **v0.4.0 is COMPLETE**
   - 322 tests pass (262 original + 60 new)
   - ruff + mypy clean on all 26 source files
   - black formatting applied to all new code
-  - `pyproject.toml` auto-discovers all 4 packages: `beta_spectrum`, `beta_spectrum.visualize`, `exp_data`, `fitter`
+  - `pyproject.toml` auto-discovers all 4 packages: `beta_spectrum`, `beta_spectrum.output`, `exp_data`, `fitter`
   - README updated with new architecture diagram and Quick Start examples
   - Version bumped to 0.4.0
 
 ### Next Immediate Step
+
 - **Track A: ⁹⁹Tc spectrum-shape analysis** — start real data processing pipeline
   - Data processing pipeline for experimental runs
   - Endpoint fitting and energy calibration