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/SKILL.md

@@ -1,11 +1,13 @@
 ---
 name: refactor
 description: |
-  Structured 9-phase refactoring workflow with three execution modes:
-  Full (all phases), Targeted (skip discovery), Quick Assessment (phases 0-2 only).
-  Supports project mode (_docs/) and standalone mode (@file.md).
+  Structured 8-phase refactoring workflow with two input modes:
+  Automatic (skill discovers issues) and Guided (input file with change list).
+  Each run gets its own subfolder in _docs/04_refactoring/.
+  Delegates code execution to the implement skill via task files in _docs/02_tasks/.
+  Additional workflow modes: Targeted (skip discovery), Quick Assessment (phases 0-2 only).
 category: evolve
-tags: [refactoring, coupling, technical-debt, performance, hardening]
+tags: [refactoring, coupling, technical-debt, performance, testability]
 trigger_phrases: ["refactor", "refactoring", "improve code", "analyze coupling", "decoupling", "technical debt", "code quality"]
 disable-model-invocation: true
 ---
@@ -16,43 +18,61 @@ Phase details live in `phases/` — read the relevant file before executing each
 
 ## Core Principles
 
-- **Preserve behavior first**: never refactor without a passing test suite
+- **Preserve behavior first**: never refactor without a passing test suite (exception: testability runs, where the goal is making code testable)
 - **Measure before and after**: every change must be justified by metrics
 - **Small incremental changes**: commit frequently, never break tests
 - **Save immediately**: write artifacts to disk after each phase
+- **Delegate execution**: all code changes go through the implement skill via task files
 - **Ask, don't assume**: when scope or priorities are unclear, STOP and ask the user
 
 ## Context Resolution
 
-Determine operating mode before any other logic runs. Announce detected mode and paths to user.
+Announce detected paths and input mode to user before proceeding.
 
-| | Project mode (default) | Standalone mode (`/refactor @file.md`) |
-|---|---|---|
-| PROBLEM_DIR | `_docs/00_problem/` | N/A |
-| SOLUTION_DIR | `_docs/01_solution/` | N/A |
-| COMPONENTS_DIR | `_docs/02_document/components/` | N/A |
-| DOCUMENT_DIR | `_docs/02_document/` | N/A |
-| REFACTOR_DIR | `_docs/04_refactoring/` | `_standalone/refactoring/` |
-| Prereqs | `problem.md` required, `acceptance_criteria.md` warn if absent | INPUT_FILE must exist and be non-empty |
+**Fixed paths:**
 
-Create REFACTOR_DIR if missing. If it already has artifacts, ask user: **resume or start fresh?**
+| Path | Location |
+|------|----------|
+| PROBLEM_DIR | `_docs/00_problem/` |
+| SOLUTION_DIR | `_docs/01_solution/` |
+| COMPONENTS_DIR | `_docs/02_document/components/` |
+| DOCUMENT_DIR | `_docs/02_document/` |
+| TASKS_DIR | `_docs/02_tasks/` |
+| REFACTOR_DIR | `_docs/04_refactoring/` |
+| RUN_DIR | `REFACTOR_DIR/NN-[run-name]/` |
+
+**Prereqs**: `problem.md` required, `acceptance_criteria.md` warn if absent.
+
+**RUN_DIR resolution**: on start, scan REFACTOR_DIR for existing `NN-*` folders. Auto-increment the numeric prefix for the new run. The run name is derived from the invocation context (e.g., `01-testability-refactoring`, `02-coupling-refactoring`). If invoked with a guided input file, derive the name from the input file name or ask the user.
+
+Create REFACTOR_DIR and RUN_DIR if missing. If a RUN_DIR with the same name already exists, ask user: **resume or start fresh?**
+
+## Input Modes
+
+| Mode | Trigger | Discovery source |
+|------|---------|-----------------|
+| Automatic | Default, no input file | Skill discovers issues from code analysis |
+| Guided | Input file provided (e.g., `/refactor @list-of-changes.md`) | Reads input file + scans code to form validated change list |
+
+Both modes produce `RUN_DIR/list-of-changes.md` (template: `templates/list-of-changes.md`). Both modes then convert that file into task files in TASKS_DIR during Phase 2.
+
+**Guided mode cleanup**: after `RUN_DIR/list-of-changes.md` is created from the input file, delete the original input file to avoid duplication.
 
 ## Workflow
 
 | Phase | File | Summary | Gate |
 |-------|------|---------|------|
-| 0 | `phases/00-baseline.md` | Collect goals, capture baseline metrics | BLOCKING: user confirms |
-| 1 | `phases/01-discovery.md` | Document components, synthesize solution | BLOCKING: user confirms |
-| 2 | `phases/02-analysis.md` | Research improvements, produce roadmap | BLOCKING: user confirms |
+| 0 | `phases/00-baseline.md` | Collect goals, create RUN_DIR, capture baseline metrics | BLOCKING: user confirms |
+| 1 | `phases/01-discovery.md` | Document components (scoped for guided mode), produce list-of-changes.md | BLOCKING: user confirms |
+| 2 | `phases/02-analysis.md` | Research improvements, produce roadmap, create epic, decompose into tasks in TASKS_DIR | BLOCKING: user confirms |
 | | | *Quick Assessment stops here* | |
-| 3 | `phases/03-safety-net.md` | Design and implement pre-refactoring tests | GATE: all tests pass |
-| 4 | `phases/04-execution.md` | Analyze coupling, execute decoupling | BLOCKING: user confirms |
-| 5 | `phases/05-hardening.md` | Technical debt, performance, security | Optional: user picks tracks |
-| 6 | `phases/06-test-sync.md` | Remove obsolete, update broken, add new tests | GATE: all tests pass |
-| 7 | `phases/07-verification.md` | Run full suite, compare metrics vs baseline | GATE: all pass, no regressions |
-| 8 | `phases/08-documentation.md` | Update `_docs/` to reflect refactored state | Skip in standalone mode |
+| 3 | `phases/03-safety-net.md` | Check existing tests or implement pre-refactoring tests (skip for testability runs) | GATE: all tests pass |
+| 4 | `phases/04-execution.md` | Delegate task execution to implement skill | GATE: implement completes |
+| 5 | `phases/05-test-sync.md` | Remove obsolete, update broken, add new tests | GATE: all tests pass |
+| 6 | `phases/06-verification.md` | Run full suite, compare metrics vs baseline | GATE: all pass, no regressions |
+| 7 | `phases/07-documentation.md` | Update `_docs/` to reflect refactored state | Skip if `_docs/02_document/` absent |
 
-**Mode detection:**
+**Workflow mode detection:**
 - "quick assessment" / "just assess" → phases 0–2
 - "refactor [specific target]" → skip phase 1 if docs exist
 - Default → all phases
@@ -61,31 +81,36 @@ At the start of execution, create a TodoWrite with all applicable phases.
 
 ## Artifact Structure
 
-All artifacts are written to REFACTOR_DIR:
+All artifacts are written to RUN_DIR:
 
 ```
 baseline_metrics.md                      Phase 0
 discovery/components/[##]_[name].md      Phase 1
 discovery/solution.md                    Phase 1
 discovery/system_flows.md                Phase 1
+list-of-changes.md                       Phase 1
 analysis/research_findings.md            Phase 2
 analysis/refactoring_roadmap.md          Phase 2
 test_specs/[##]_[test_name].md           Phase 3
-coupling_analysis.md                     Phase 4
 execution_log.md                         Phase 4
-hardening/{technical_debt,performance,security}.md   Phase 5
-test_sync/{obsolete_tests,updated_tests,new_tests}.md  Phase 6
-verification_report.md                   Phase 7
-doc_update_log.md                        Phase 8
+test_sync/{obsolete_tests,updated_tests,new_tests}.md  Phase 5
+verification_report.md                   Phase 6
+doc_update_log.md                        Phase 7
 FINAL_report.md                          after all phases
 ```
 
+Task files produced during Phase 2 go to TASKS_DIR (not RUN_DIR):
+```
+TASKS_DIR/[JIRA-ID]_refactor_[short_name].md
+TASKS_DIR/_dependencies_table.md (appended)
+```
+
 **Resumability**: match existing artifacts to phases above, resume from next incomplete phase.
 
 ## Final Report
 
-After all phases complete, write `REFACTOR_DIR/FINAL_report.md`:
-mode used, phases executed, baseline vs final metrics, changes summary, remaining items, lessons learned.
+After all phases complete, write `RUN_DIR/FINAL_report.md`:
+mode used (automatic/guided), input mode, phases executed, baseline vs final metrics, changes summary, remaining items, lessons learned.
 
 ## Escalation Rules
 
@@ -97,3 +122,4 @@ mode used, phases executed, baseline vs final metrics, changes summary, remainin
 | Performance vs readability trade-off | **ASK user** |
 | No test suite or CI exists | **WARN user**, suggest safety net first |
 | Security vulnerability found | **WARN user** immediately |
+| Implement skill reports failures | **ASK user** — review batch reports |