Update test results directory structure and enhance Docker configurations

- Modified `.gitignore` to reflect the new path for test results.
- Updated `docker-compose.test.yml` to mount the correct test results directory.
- Adjusted `Dockerfile.test` to set the `PYTHONPATH` and ensure test results are saved in the updated location.
- Added `boto3` and `netron` to `requirements-test.txt` to support new functionalities.
- Updated `pytest.ini` to include the new `pythonpath` for test discovery.

These changes streamline the testing process and ensure compatibility with the updated directory structure.

.cursor/skills/refactor/phases/00-baseline.md

@@ -1,7 +1,7 @@
 # Phase 0: Context & Baseline
 
 **Role**: Software engineer preparing for refactoring
-**Goal**: Collect refactoring goals and capture baseline metrics
+**Goal**: Collect refactoring goals, create run directory, capture baseline metrics
 **Constraints**: Measurement only — no code changes
 
 ## 0a. Collect Goals
@@ -14,7 +14,18 @@ If PROBLEM_DIR files do not yet exist, help the user create them:
 
 Store in PROBLEM_DIR.
 
-## 0b. Capture Baseline
+## 0b. Create RUN_DIR
+
+1. Scan REFACTOR_DIR for existing `NN-*` folders
+2. Auto-increment the numeric prefix (e.g., if `01-testability-refactoring` exists, next is `02-...`)
+3. Determine the run name:
+   - If guided mode with input file: derive from input file name or context (e.g., `01-testability-refactoring`)
+   - If automatic mode: ask user for a short run name, or derive from goals (e.g., `01-coupling-refactoring`)
+4. Create `REFACTOR_DIR/NN-[run-name]/` — this is RUN_DIR for the rest of the workflow
+
+Announce RUN_DIR path to user.
+
+## 0c. Capture Baseline
 
 1. Read problem description and acceptance criteria
 2. Measure current system metrics using project-appropriate tools:
@@ -31,10 +42,11 @@ Store in PROBLEM_DIR.
 3. Create functionality inventory: all features/endpoints with status and coverage
 
 **Self-verification**:
+- [ ] RUN_DIR created with correct auto-incremented prefix
 - [ ] All metric categories measured (or noted as N/A with reason)
 - [ ] Functionality inventory is complete
 - [ ] Measurements are reproducible
 
-**Save action**: Write `REFACTOR_DIR/baseline_metrics.md`
+**Save action**: Write `RUN_DIR/baseline_metrics.md`
 
 **BLOCKING**: Present baseline summary to user. Do NOT proceed until user confirms.