Add ./output/ directory for debug verification artifacts and update development workflow

- Create ./output/ with .gitkeep for test run outputs
- Add output/* to .gitignore (negated .gitkeep)
- Add §4.5 Debug Verification to DEVELOPMENT.md: final step of each dev iteration
  - Run bs_pnpi -vv with full parameter consistency checks
  - Required debug logging per component documented
  - Example commands and success criteria
- Update Agent Instructions and Release Checklist
- Mark B8.3 debug verification framework as completed in TODO.md

.gitignore

@@ -81,6 +81,8 @@ ipython_config.py
 # data/
 outputs/
 results/
+output/*
+!output/.gitkeep
 *.npy
 *.npz
 *.h5

DEVELOPMENT.md

@@ -111,6 +111,103 @@ Notebooks in `notebooks/` are executed as pytest tests using `nbmake`. This ensu
    pytest notebooks/ --nbmake  # or just `pytest` (includes notebooks/)
    ```
 
+______________________________________________________________________
+
+### 4.5. Debug Verification (Final Step of Each Dev Iteration)
+
+After all quality gates pass, run a **debug-level verification** as the final step of every development iteration. This catches configuration mismatches, missing parameter propagation, and silent logic errors before merging.
+
+**Purpose:** Verify that all parameters (endpoint energy, energy grid, Z, A, physical constants) are consistent throughout the pipeline, and that every spectrum component emits sufficient debug logging for explicit comparison.
+
+**Procedure:**
+
+1. **Run `bs_pnpi` with `-vv` (DEBUG logging) and output to `./output/`:**
+   ```bash
+   bs_pnpi --nuclide Tc99 -vv --output ./output/verification.csv
+   ```
+
+2. **Capture full debug output to a log file for analysis:**
+   ```bash
+   bs_pnpi --nuclide Tc99 -vv --output ./output/verification.csv --log-file ./output/debug.log 2>&1 | tee ./output/debug_stdout.log
+   ```
+
+3. **Verify consistency of key parameters in the debug output:**
+
+   | Parameter | What to check | Where to find it |
+   |---|---|---|
+   | `endpoint_MeV` | Matches expected Q-value | CLI dry-run, config creation, energy grid |
+   | `Z_parent` / `Z_daughter` | Consistent across all components | Component init logs |
+   | `A_number` | Consistent across all components | Component init logs |
+   | `e_step_MeV` | Matches grid size × (endpoint - e_step) | Energy grid creation |
+   | `W0` (endpoint in natural units) | `W0 = 1.0 + endpoint_MeV / m_e` | PhaseSpace init |
+   | Physical constants | `m_e = 0.51099895` MeV, `α = 1/137.036` | Constants module, Fermi function |
+   | Energy grid bounds | `e_step` to `endpoint - e_step` | `get_energy_grid()` output |
+
+4. **Verify each component's debug logging:**
+
+   Every enabled component must log its initialization parameters and a representative evaluation. Check the debug output for entries like:
+
+   ```
+   DEBUG ... Initializing PhaseSpace: W0=1.57664, transition_type=A, m_e=1.0
+   DEBUG ... Evaluating PhaseSpace at 294 energy points
+   DEBUG ... PhaseSpace range: [min=..., max=...]
+   ```
+
+   Required log entries per component:
+
+   | Component | Must log |
+   |---|---|
+   | `PhaseSpace` | `W0`, `transition_type`, `m_e`, `m_nu`, energy range |
+   | `FermiFunction` | `Z`, `A`, `α`, Coulomb approximation used |
+   | `FiniteSizeL0` | `Z`, `A`, nuclear radius `R`, L0 approximation |
+   | `ChargeDistributionU` | `Z`, `A`, charge radius, U correction range |
+   | `ScreeningCorrection` | `Z_parent`, screening model, S(Z,W) range |
+   | `ExchangeCorrection` | `Z_parent`, Hayen coefficients used, X(Z,W) range |
+   | `RadiativeCorrection` | `W0`, `δ_r` formula, resummation flag, `delta_cut` value |
+
+5. **Report any missing logging:**
+
+   If a component's debug output does not allow explicit verification of its parameters or computed range, **add logging to that component** before the iteration is considered complete. The goal is that a developer (or an LLM) reading the debug log can reconstruct every parameter and verify correctness without reading source code.
+
+6. **Save debug artifacts to `./output/`:**
+
+   After verification, ensure all artifacts are in `./output/`:
+   - `debug_stdout.log` — full stdout+stderr from `bs_pnpi -vv`
+   - `debug.log` — log file output (if `--log-file` was used)
+   - `verification.csv` — the spectrum CSV with metadata header
+   - `verification.png` — analysis plot (if `--plot` was used)
+
+   These files serve as a **verifiable record** of the last working state and can be used for regression comparison.
+
+**Example verification command:**
+
+```bash
+# Full debug run with all outputs
+bs_pnpi --nuclide Tc99 -vv \
+    --output ./output/verification.csv \
+    --plot ./output/verification.png \
+    --log-file ./output/debug.log 2>&1 | tee ./output/debug_stdout.log
+
+# Quick parameter extraction from debug log
+grep -E '(Initializing|Evaluating|W0=|Z=|endpoint|e_step|PhaseSpace|Fermi|FiniteSize|Screening|Exchange|Radiative)' ./output/debug_stdout.log
+```
+
+**Success criteria:**
+
+- [ ] All parameters (Z, A, endpoint, e_step, W0) appear consistently in debug output
+- [ ] Each enabled component logs its initialization parameters
+- [ ] Each enabled component logs its evaluation energy range
+- [ ] Physical constants match expected values
+- [ ] No silent parameter coercion or unit conversion errors detected
+- [ ] All artifacts saved to `./output/`
+
+**If any check fails:**
+
+1. Add missing debug logging to the component
+2. Fix any parameter mismatch
+3. Re-run the verification until all checks pass
+4. Only then consider the iteration complete
+
 ## 5. Agent Instructions
 
 When working on this project, agents must:
@@ -123,6 +220,7 @@ When working on this project, agents must:
 6. **Work on a dev branch** — create `dev/<description>` and switch to it
 7. **Run quality gates** after making changes and report results
 8. **Update docs** when changing public API or adding features
+9. **Run debug verification** (`bs_pnpi -vv`) as the final step of each iteration, saving all artifacts to `./output/` and verifying parameter consistency across all components
 
 ## 6. Release Checklist
 
@@ -130,6 +228,8 @@ When working on this project, agents must:
 - [ ] Code is formatted (`black --check`)
 - [ ] No lint errors (`ruff check`)
 - [ ] Type checks pass (`mypy`)
+- [ ] Debug verification passes (`bs_pnpi -vv`) — all parameters consistent, all components logged
+- [ ] Debug artifacts saved to `./output/` (debug_stdout.log, verification.csv, etc.)
 - [ ] Update version in `pyproject.toml`
 - [ ] Update `Development Status` section in `README.md`
 - [ ] Update `TODO.md` marking corresponding items as complete.

TODO.md

@@ -178,6 +178,8 @@ ______________________________________________________________________
 - [x] Add `--dry-run` option to validate input and display resolved parameters without calculation
 - [x] Add `--version` flag
 - [x] Add `-q/--quiet` flag to suppress terminal output
+- [x] Add `./output/` directory for debug verification artifacts (gitignored except `.gitkeep`)
+- [x] Add debug verification step to development workflow: `bs_pnpi -vv` with parameter consistency checks across all components, documented in DEVELOPMENT.md §4.5
 
 ______________________________________________________________________
 
@@ -205,6 +207,6 @@ ______________________________________________________________________
 **Version:** 0.3.0\
 **Implemented:** Phase space, Fermi function, finite size, screening, exchange, radiative corrections (with delta_cut resummation). Detector response module with analytical models (Gaussian, Gaussian+tail, Tikhonov), convolution API, declarative config integration. χ² curve fitting framework (CurveFitter) with confidence intervals, profile likelihood, and correlation analysis. C(W) shape factor extraction pipeline (CWExtractor) with Kurie plot analysis, parametrized fitting, and g_V/g_A extraction. CLI interface (`bs_pnpi`) with paceENSDF integration, structured logging (-v/-vv/-q), --dry-run, --version, --log-file. CSV metadata headers. JSON input with full detector param support. Comprehensive test suite (195 tests). Notebook quality control with nbmake and auto-save plot hooks.
 
-**Completed:** A2 — detector response function and convolution routines. A4 — fitter routine and C(W) extraction pipeline. B2 — input flexibility (JSON input, ENSDF auto-population). B8 — CLI & output improvements (logging, CSV headers, dry-run, version). B8.2 — CLI refinement: removed --mode, --transition-type, --decay-index flags; clarified units (MeV everywhere); enhanced logging (INFO shows components, DEBUG shows internals); CSV headers use element notation (Tc99 -> Ru99).
+**Completed:** A2 — detector response function and convolution routines. A4 — fitter routine and C(W) extraction pipeline. B2 — input flexibility (JSON input, ENSDF auto-population). B8 — CLI & output improvements (logging, CSV headers, dry-run, version). B8.2 — CLI refinement: removed --mode, --transition-type, --decay-index flags; clarified units (MeV everywhere); enhanced logging (INFO shows components, DEBUG shows internals); CSV headers use element notation (Tc99 -> Ru99). B8.3 — debug verification framework: `./output/` directory for artifacts, development workflow step 4.5 with `-vv` parameter consistency checks across all components.
 
 **Next immediate step:** A3 — data processing pipeline for experimental spectra (background subtraction, energy calibration, dead-time correction, pulse pile-up correction).