Refactor constants management to use Pydantic BaseModel for configuration

- Replaced module-level path variables in constants.py with a structured Pydantic Config class.
- Updated all relevant modules (train.py, augmentation.py, exports.py, dataset-visualiser.py, manual_run.py) to access paths through the new config structure.
- Fixed bugs related to image processing and model saving.
- Enhanced test infrastructure to accommodate the new configuration approach.

This refactor improves code maintainability and clarity by centralizing configuration management.

.cursor/skills/autopilot/flows/existing-code.md

@@ -11,7 +11,7 @@ Workflow for projects with an existing codebase. Starts with documentation, prod
 | 3 | Decompose Tests | decompose/SKILL.md (tests-only) | Step 1t + Step 3 + Step 4 |
 | 4 | Implement Tests | implement/SKILL.md | (batch-driven, no fixed sub-steps) |
 | 5 | Run Tests | test-run/SKILL.md | Steps 1–4 |
-| 6 | Refactor | refactor/SKILL.md | Phases 0–5 (6-phase method) |
+| 6 | Refactor | refactor/SKILL.md | Phases 0–6 (7-phase method) (optional) |
 | 7 | New Task | new-task/SKILL.md | Steps 1–8 (loop) |
 | 8 | Implement | implement/SKILL.md | (batch-driven, no fixed sub-steps) |
 | 9 | Run Tests | test-run/SKILL.md | Steps 1–4 |
@@ -75,19 +75,31 @@ Verifies the implemented test suite passes before proceeding to refactoring. The
 
 ---
 
-**Step 6 — Refactor**
-Condition: the autopilot state shows Step 5 (Run Tests) is completed AND `_docs/04_refactoring/FINAL_report.md` does not exist
+**Step 6 — Refactor (optional)**
+Condition: the autopilot state shows Step 5 (Run Tests) is completed AND the autopilot state does NOT show Step 6 (Refactor) as completed or skipped AND `_docs/04_refactoring/FINAL_report.md` does not exist
 
-Action: Read and execute `.cursor/skills/refactor/SKILL.md`
+Action: Present using Choose format:
 
-The refactor skill runs the full 6-phase method using the implemented tests as a safety net.
+```
+══════════════════════════════════════
+ DECISION REQUIRED: Refactor codebase before adding new features?
+══════════════════════════════════════
+ A) Run refactoring (recommended if code quality issues were noted during documentation)
+ B) Skip — proceed directly to New Task
+══════════════════════════════════════
+ Recommendation: [A or B — base on whether documentation
+ flagged significant code smells, coupling issues, or
+ technical debt worth addressing before new development]
+══════════════════════════════════════
+```
 
-If `_docs/04_refactoring/` has phase reports, the refactor skill detects completed phases and continues.
+- If user picks A → Read and execute `.cursor/skills/refactor/SKILL.md`. The refactor skill runs the full method using the implemented tests as a safety net. If `_docs/04_refactoring/` has phase reports, the refactor skill detects completed phases and continues. After completion, auto-chain to Step 7 (New Task).
+- If user picks B → Mark Step 6 as `skipped` in the state file, auto-chain to Step 7 (New Task).
 
 ---
 
 **Step 7 — New Task**
-Condition: the autopilot state shows Step 6 (Refactor) is completed AND the autopilot state does NOT show Step 7 (New Task) as completed
+Condition: the autopilot state shows Step 6 (Refactor) is completed or skipped AND the autopilot state does NOT show Step 7 (New Task) as completed
 
 Action: Read and execute `.cursor/skills/new-task/SKILL.md`
 
@@ -198,8 +210,8 @@ Action: The project completed a full cycle. Present status and loop back to New
 | Test Spec (2) | Auto-chain → Decompose Tests (3) |
 | Decompose Tests (3) | **Session boundary** — suggest new conversation before Implement Tests |
 | Implement Tests (4) | Auto-chain → Run Tests (5) |
-| Run Tests (5, all pass) | Auto-chain → Refactor (6) |
-| Refactor (6) | Auto-chain → New Task (7) |
+| Run Tests (5, all pass) | Auto-chain → Refactor choice (6) |
+| Refactor (6, done or skipped) | Auto-chain → New Task (7) |
 | New Task (7) | **Session boundary** — suggest new conversation before Implement |
 | Implement (8) | Auto-chain → Run Tests (9) |
 | Run Tests (9, all pass) | Auto-chain → Security Audit choice (10) |
@@ -218,7 +230,7 @@ Action: The project completed a full cycle. Present status and loop back to New
  Step 3   Decompose Tests     [DONE (N tasks) / IN PROGRESS / NOT STARTED / FAILED (retry N/3)]
  Step 4   Implement Tests     [DONE / IN PROGRESS (batch M) / NOT STARTED / FAILED (retry N/3)]
  Step 5   Run Tests           [DONE (N passed, M failed) / IN PROGRESS / NOT STARTED / FAILED (retry N/3)]
- Step 6   Refactor            [DONE / IN PROGRESS (phase N) / NOT STARTED / FAILED (retry N/3)]
+ Step 6   Refactor            [DONE / SKIPPED / IN PROGRESS (phase N) / NOT STARTED / FAILED (retry N/3)]
  Step 7   New Task            [DONE (N tasks) / IN PROGRESS / NOT STARTED / FAILED (retry N/3)]
  Step 8   Implement           [DONE / IN PROGRESS (batch M of ~N) / NOT STARTED / FAILED (retry N/3)]
  Step 9   Run Tests           [DONE (N passed, M failed) / IN PROGRESS / NOT STARTED / FAILED (retry N/3)]