# Session Log 8: Comprehensive Workspace Cleanup and Organization for Paper Readiness

**Date**: August 31, 2025  
**Focus**: Complete reorganization of idea_14_workspace directory structure, systematic cleanup of all experimental outputs, and preparation for paper writing phase with emphasis on reproducibility and transparency

## Session Overview

This session focused on transforming the research workspace from an active development environment to a clean, paper-ready archive. The key achievement was systematically organizing all experimental outputs, removing unnecessary development artifacts, and ensuring complete reproducibility through proper file organization and Modal storage synchronization. This cleanup represents the transition from experimentation to paper writing.

## Session Context and Continuation Point

**Previous Status (Session 7)**: H5 evaluation was completed with two-phase approach. All major hypotheses (H1-H6) had been executed with varying degrees of completion. The workspace contained mixed development artifacts, test files, and experimental outputs without clear organization.

**Current Session Goal**: Prepare the entire workspace for paper writing by cleaning, organizing, and ensuring all experimental results are properly structured and accessible.

## Major Accomplishments

### 1. Complete Directory Reorganization

**Root-Level Changes:**
- Moved `session_logs/` → `../claude_code_session_logs/` (parent directory)
- Moved `papers/` → `../papers/` (parent directory)
- Moved `reports/` → `../archive/` (development checkpoint reports)
- Deleted `logs/setup.log` and `requirements.txt` (redundant)

**Source Code Organization:**
- Created logical subdirectories in `src/`:
  - `core/` - Core infrastructure (semantic_entropy.py, baseline_metrics.py, etc.)
  - `experiments/h1-h7/` - Hypothesis-specific experiment scripts
  - `tests/` → `archived_code/tests/` (moved test files to archive)
- Updated all import statements across 20+ files to reflect new structure

**Archive Reorganization:**
- Renamed `archive/` → `archived_code/` within workspace
- Created subdirectories:
  - `tests/` (4 test scripts)
  - `data_processing/` (8 validation/processing scripts)
  - `legacy_utilities/` (4 superseded utilities)

### 2. Data Directory Cleanup

**Processed Data Reduction (81% size reduction):**
- Started with 10 files (2,447 samples)
- Removed unused files:
  - `wildguard_test.jsonl` (1,725 samples - never used)
  - `jbb_h2_test.jsonl`, `jbb_calibration.jsonl`, `jbb_benign_hard_test.jsonl`
  - `harmbench_contextual_test.jsonl` (duplicate format)
- Final: 5 essential files (462 samples) for full reproducibility

**Data Organization:**
- Moved `manifests/` → `data/manifests/` (better logical grouping)
- Kept only datasets actively used in experiments

### 3. Experimental Outputs Standardization

**H1 Reorganization (9 files):**
```
h1/
├── response_generation/  (responses + generation logs)
├── scoring/             (scores + scoring logs)
└── evaluation/          (final results)
```

**H2 Structure (Template - already organized):**
```
h2/
├── response_generation/
├── scoring/
└── evaluation/
```

**H3 Reorganization (5 files):**
```
h3/
├── results/             (analysis results)
├── per_prompt_analysis/ (detailed per-prompt data)
└── logs/               (execution logs)
```

**H4 Reorganization (6 files):**
```
h4/
├── response_generation/ (topup responses)
├── evaluation/         (brittleness results + report)
└── logs/              (execution logs)
```

**H5 Completion & Organization (14 files):**
```
h5/
├── paraphrase_generation/
├── response_generation/
├── scoring/
└── evaluation/         (NEWLY DOWNLOADED from Modal)
```

**H6 Reorganization (16 files):**
```
h6/
├── llama-h1-jailbreakbench/
├── llama-h2-harmbench/
├── qwen-h1-jailbreakbench/
└── qwen-h2-harmbench/
```
Each containing: results.json, predictions.jsonl, report.md, logs.txt

### 4. Modal Storage Synchronization

**Critical Downloads Completed:**
- H4: Downloaded all brittleness evaluation files (6 files)
- H5: **Discovered and downloaded missing evaluation files**:
  - `h5_robustness_evaluation.json`
  - `h5_paraphrase_degradation_report.md`
- H6: Downloaded all qualitative audit files (16 files across 4 model-dataset combinations)

**Verification:** All experimental outputs now present locally, no missing components

## Key Technical Decisions

### 1. Import Path Updates
- Systematically updated 20+ Python files to use new `src.core.*` and `src.experiments.*` paths
- Verified no broken dependencies through grep searches
- Ensured Modal compatibility with updated structure

### 2. File Preservation Strategy
- **Archived** rather than deleted valuable process documentation
- **Deleted** only truly redundant files (empty directories, unused large datasets)
- **Preserved** all files contributing to reproducibility

### 3. H6 Special Organization
- Created model-dataset specific subdirectories for clarity
- Recognized multiple experimental runs (different consistency confound rates)
- Kept all variants for methodological transparency

## Issues Resolved

### 1. Missing H5 Evaluation Files
**Problem**: H5 appeared incomplete with no evaluation outputs
**Solution**: Found and downloaded evaluation files from Modal storage
**Result**: H5 now complete with full pipeline outputs

### 2. H6 File Duplication Confusion
**Problem**: Multiple files with similar names but different results
**Investigation**: Discovered these represent different experimental runs/parameters
**Decision**: Keep all files as they document experimental evolution

### 3. Data File Redundancy
**Problem**: Multiple JBB and HarmBench variants causing confusion
**Solution**: Removed unused variants, kept only actively used datasets
**Impact**: 81% reduction in data footprint while maintaining reproducibility

## Final Workspace Statistics

**Total Structure:**
- **Core directories**: 5 (src, data, configs, outputs, archived_code)
- **Hypothesis outputs**: H1-H6 complete, H7 not executed
- **Total output files**: ~60 files across all hypotheses
- **Data files**: 5 essential datasets (462 samples)
- **Archived files**: 16 development artifacts properly organized

**Paper Readiness Checklist:**
- ✅ All experimental outputs organized by hypothesis
- ✅ Clear separation of results, logs, and intermediate files
- ✅ Data files reduced to essential set
- ✅ Import paths updated and verified
- ✅ Development artifacts archived
- ✅ Modal storage synchronized
- ✅ Directory structure optimized for paper writing

## Next Steps for Paper Writing

1. **Results Extraction**: All hypothesis results now in standardized locations
2. **Reproducibility**: Clean workspace with only essential files
3. **Documentation**: Session logs provide complete experimental history
4. **Missing Work**: H7 (SOTA comparison) not yet executed

## Continuation Notes

The workspace is now in optimal condition for paper writing. All experimental artifacts are properly organized, development clutter has been removed, and the structure clearly reflects the experimental pipeline from H1 through H6. The next session should focus on either H7 execution or beginning the paper writing process with the clean, organized results now available.

**Key Achievement**: Transformed a working research directory into a publication-ready archive while maintaining complete reproducibility and transparency.