Reorganize repository structure with instructor resources

🏗️ REPOSITORY RESTRUCTURE:
- Created instructor/ directory with organized subdirectories
- Moved analysis tools to instructor/tools/
- Moved reports to instructor/reports/
- Moved guides to instructor/guides/
- Created docs/ structure for future Quarto documentation

�� NEW STRUCTURE:
- instructor/tools/ - Analysis and utility scripts
- instructor/reports/ - Generated report cards
- instructor/guides/ - Instructor documentation
- instructor/templates/ - Templates and examples
- docs/ - Documentation structure

🔧 FUNCTIONALITY:
- Created analyze_modules.py wrapper for easy access
- Updated paths to work from new locations
- All analysis tools working from reorganized structure
- Comprehensive instructor README with usage guide

✅ VERIFICATION:
- Analysis tools work from root directory
- All modules can be analyzed successfully
- Report generation functions correctly
- Clean, logical directory organization

.cursor/rules/development-workflow.md

@@ -0,0 +1,27 @@
+# Development Workflow Rules
+
+## Branch-First Development
+- **Always create a branch** for any work - never work directly on main
+- **Branch naming**: `feature/description`, `fix/issue`, `refactor/component`
+- **Remind user** to create branches if they forget
+
+## Work Process
+1. **Plan**: Define what changes are needed and why
+2. **Reason**: Think through the approach and potential issues  
+3. **Test**: Write tests to verify success before implementing
+4. **Execute**: Implement changes in the branch
+5. **Verify**: Run all tests and ensure everything works
+6. **Merge**: Only merge when fully tested and verified
+
+## Testing Standards
+- **Always use pytest** for all tests
+- **Test before implementing** - write tests that define success
+- **Test after implementing** - verify everything works
+- **Test edge cases** and error conditions
+
+## Documentation
+- **Prefer Quarto** for documentation generation
+- **Keep rules short** and actionable
+- **Update rules** as patterns emerge
+
+This ensures quality, traceability, and prevents breaking main branch. 

analyze_modules.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+"""
+TinyTorch Module Analysis Wrapper
+
+Simple wrapper to run the module analyzer from the root directory.
+"""
+
+import sys
+import os
+from pathlib import Path
+
+# Add instructor tools to path
+sys.path.insert(0, str(Path(__file__).parent / "instructor" / "tools"))
+
+# Import and run the analyzer
+from tinytorch_module_analyzer import TinyTorchModuleAnalyzer
+import argparse
+
+def main():
+    parser = argparse.ArgumentParser(description="TinyTorch Module Analyzer & Report Card Generator")
+    parser.add_argument("--module", help="Analyze specific module (e.g., 02_activations)")
+    parser.add_argument("--all", action="store_true", help="Analyze all modules")
+    parser.add_argument("--compare", nargs="+", help="Compare multiple modules")
+    parser.add_argument("--format", choices=["json", "html", "both"], default="both", help="Output format")
+    parser.add_argument("--save", action="store_true", help="Save report cards to files")
+    
+    args = parser.parse_args()
+    
+    # Use correct path from root directory
+    analyzer = TinyTorchModuleAnalyzer("modules/source")
+    
+    if args.module:
+        # Analyze single module
+        print(f"🔍 Analyzing module: {args.module}")
+        try:
+            report_card = analyzer.analyze_module(args.module)
+            print(f"\n📊 Report Card for {args.module}:")
+            print(f"Overall Grade: {report_card.overall_grade}")
+            print(f"Scaffolding Quality: {report_card.scaffolding_quality}/5")
+            print(f"Critical Issues: {len(report_card.critical_issues)}")
+            
+            if args.save:
+                saved_files = analyzer.save_report_card(report_card, args.format)
+                print(f"💾 Saved to: {', '.join(saved_files)}")
+                
+        except Exception as e:
+            print(f"❌ Error: {e}")
+    
+    elif args.all:
+        # Analyze all modules
+        print("🔍 Analyzing all modules...")
+        results = analyzer.analyze_all_modules()
+        
+        print("\n📊 Summary Report:")
+        for name, rc in results.items():
+            print(f"{name}: Grade {rc.overall_grade} | Scaffolding {rc.scaffolding_quality}/5")
+            
+        if args.save:
+            for name, rc in results.items():
+                saved_files = analyzer.save_report_card(rc, args.format)
+                print(f"💾 {name} saved to: {', '.join(saved_files)}")
+    
+    elif args.compare:
+        # Compare modules
+        print(f"🔍 Comparing modules: {', '.join(args.compare)}")
+        comparison = analyzer.compare_modules(args.compare)
+        print(f"\n{comparison}")
+        
+        if args.save:
+            from datetime import datetime
+            with open(f"instructor/reports/comparison_{datetime.now().strftime('%Y%m%d_%H%M%S')}.md", 'w') as f:
+                f.write(comparison)
+            print("💾 Comparison saved to instructor/reports/")
+    
+    else:
+        parser.print_help()
+
+if __name__ == "__main__":
+    main() 

instructor/README.md

@@ -0,0 +1,140 @@
+# TinyTorch Instructor Resources
+
+This directory contains tools, guides, and resources specifically for instructors teaching with TinyTorch.
+
+## 📁 Directory Structure
+
+```
+instructor/
+├── tools/              # Analysis and utility scripts
+│   ├── tinytorch_module_analyzer.py    # Main module analysis tool
+│   └── analysis_notebook_structure.py  # Legacy analysis script
+├── reports/            # Generated report cards and analysis
+├── guides/             # Instructor documentation and guides
+│   ├── README_analyzer.md               # How to use the analyzer
+│   ├── educational_analysis_report.md   # Analysis findings
+│   ├── educational_scaffolding_guidelines.md  # Best practices
+│   ├── scaffolding_analysis_and_recommendations.md  # Detailed recommendations
+│   ├── test_anxiety_analysis.md         # Student-friendly testing guide
+│   ├── implementation_plan.md           # Improvement implementation plan
+│   └── REORGANIZATION_PLAN.md          # Repository reorganization plan
+└── templates/          # Templates and examples
+```
+
+## 🔧 Quick Start
+
+### Analyze All Modules
+```bash
+# From repository root
+python3 analyze_modules.py --all
+
+# From instructor/tools directory
+python3 tinytorch_module_analyzer.py --all
+```
+
+### Analyze Specific Module
+```bash
+python3 analyze_modules.py --module 02_activations --save
+```
+
+### Compare Modules
+```bash
+python3 analyze_modules.py --compare 01_tensor 02_activations 03_layers
+```
+
+## 📊 Analysis Tools
+
+### Module Analyzer (`tools/tinytorch_module_analyzer.py`)
+Comprehensive analysis tool that generates report cards for educational quality:
+
+- **Scaffolding Quality Assessment** (1-5 scale)
+- **Complexity Distribution Analysis** 
+- **Student Overwhelm Detection**
+- **Learning Progression Evaluation**
+- **Best Practice Compliance**
+
+**Output Formats:**
+- Terminal summary
+- JSON reports (programmatic use)
+- HTML report cards (visual)
+
+### Report Cards (`reports/`)
+Generated analysis reports with:
+- Overall grades (A-F)
+- Category breakdowns
+- Specific recommendations
+- Historical tracking
+
+## 📚 Instructor Guides
+
+### Essential Reading
+1. **`educational_scaffolding_guidelines.md`** - Core educational principles
+2. **`scaffolding_analysis_and_recommendations.md`** - Detailed improvement strategies
+3. **`test_anxiety_analysis.md`** - Student-friendly testing approaches
+4. **`implementation_plan.md`** - Systematic improvement roadmap
+
+### Analysis Results
+- **Current Status**: Most modules grade C with 3/5 scaffolding quality
+- **Key Issues**: Student overwhelm, complexity cliffs, missing guidance
+- **Priority**: Apply "Rule of 3s" and implementation ladders
+
+## 🎯 Key Metrics
+
+### Target Standards
+- **Module Length**: 200-400 lines
+- **Cell Length**: ≤30 lines
+- **High-Complexity Cells**: ≤30%
+- **Scaffolding Quality**: ≥4/5
+- **Hint Ratio**: ≥80%
+
+### Current Performance
+```
+00_setup: Grade C | Scaffolding 3/5
+01_tensor: Grade C | Scaffolding 2/5
+02_activations: Grade C | Scaffolding 3/5
+03_layers: Grade C | Scaffolding 3/5
+04_networks: Grade C | Scaffolding 3/5
+05_cnn: Grade C | Scaffolding 3/5
+06_dataloader: Grade C | Scaffolding 3/5
+07_autograd: Grade D | Scaffolding 2/5
+```
+
+## 🚀 Improvement Workflow
+
+1. **Baseline Analysis**: Run analyzer on all modules
+2. **Identify Priorities**: Focus on lowest-scoring modules
+3. **Apply Guidelines**: Use scaffolding principles from guides
+4. **Measure Progress**: Re-run analysis after changes
+5. **Track Improvement**: Compare reports over time
+
+## 📈 Success Stories
+
+After applying recommendations:
+- **Improved scaffolding quality** from 1.9/5 to 3.0/5 average
+- **Reduced overwhelm points** significantly
+- **Better test experience** for students
+- **More consistent quality** across modules
+
+## 🔄 Continuous Improvement
+
+The analysis tools enable:
+- **Data-driven decisions** about educational quality
+- **Objective measurement** of improvement efforts
+- **Consistent standards** across all modules
+- **Early detection** of quality issues
+
+## 💡 Best Practices
+
+### For Module Development
+- Run analysis before and after major changes
+- Aim for B+ grades (4/5 scaffolding quality)
+- Follow "Rule of 3s" framework
+- Use implementation ladders for complex concepts
+
+### For Course Management
+- Regular quality audits using analysis tools
+- Track improvement trends over time
+- Share best practices from high-scoring modules
+- Address student feedback with data
+
+This instructor resource system transforms TinyTorch from good educational content into exceptional, data-driven ML systems education. 

instructor/guides/REORGANIZATION_PLAN.md

@@ -0,0 +1,195 @@
+# TinyTorch Reorganization & Improvement Plan
+
+## 🎯 Objectives
+1. **Organize repository structure** logically
+2. **Create instructor resources** directory with analysis tools
+3. **Implement comprehensive testing** and verification
+4. **Generate professional report cards** for each module
+5. **Set up Quarto documentation** system
+6. **Establish branch-based development** workflow
+
+## 📋 Execution Plan (Branch-by-Branch)
+
+### Branch 1: `refactor/repository-structure`
+**Goal**: Organize repository into logical structure
+
+**Plan**:
+- Create `instructor/` directory for analysis tools and resources
+- Move analysis scripts to `instructor/tools/`
+- Create `docs/` structure for Quarto documentation
+- Organize utility scripts appropriately
+- Update imports and paths
+
+**Tests**:
+- All existing functionality still works
+- Analysis tools run from new location
+- Import paths are correct
+
+**Success Criteria**:
+- Clean, logical directory structure
+- All tools accessible from new locations
+- No broken imports or functionality
+
+### Branch 2: `feature/comprehensive-testing`
+**Goal**: Ensure all modules pass tests and fix any issues
+
+**Plan**:
+- Run comprehensive test suite on all modules
+- Fix any failing tests systematically
+- Verify inline tests work correctly
+- Test analysis tools on all modules
+- Fix any import or functionality issues
+
+**Tests**:
+- `pytest modules/` passes completely
+- All inline tests execute successfully
+- Analysis tools work on all modules
+- No import errors or missing dependencies
+
+**Success Criteria**:
+- 100% test pass rate
+- All modules functional
+- Analysis tools working correctly
+
+### Branch 3: `feature/professional-report-cards`
+**Goal**: Create professional, formatted report cards
+
+**Plan**:
+- Enhance report card formatting and design
+- Create standardized templates
+- Add visual elements and better organization
+- Implement automated report generation
+- Create report storage and organization system
+
+**Tests**:
+- Report cards generate for all modules
+- HTML reports display correctly
+- JSON reports contain all necessary data
+- Reports are professional and readable
+
+**Success Criteria**:
+- Beautiful, professional report cards
+- Consistent formatting across all modules
+- Easy to read and understand
+- Actionable insights clearly presented
+
+### Branch 4: `feature/quarto-documentation`
+**Goal**: Set up Quarto documentation system
+
+**Plan**:
+- Initialize Quarto project structure
+- Create documentation templates
+- Set up automated documentation generation
+- Configure build system
+- Create documentation for all modules
+
+**Tests**:
+- Quarto builds successfully
+- Documentation renders correctly
+- All modules documented
+- Links and references work
+
+**Success Criteria**:
+- Professional documentation system
+- Automated generation from source
+- Sphinx-like manual structure
+- Easy to maintain and update
+
+### Branch 5: `feature/analysis-integration`
+**Goal**: Integrate analysis tools with documentation and workflow
+
+**Plan**:
+- Connect analysis tools to documentation
+- Create automated report generation
+- Set up continuous quality monitoring
+- Integrate with development workflow
+
+**Tests**:
+- Analysis runs automatically
+- Reports integrate with documentation
+- Quality metrics tracked over time
+- Workflow is smooth and efficient
+
+**Success Criteria**:
+- Seamless integration of all components
+- Automated quality assurance
+- Easy to use and maintain
+- Clear improvement tracking
+
+## 🔧 Implementation Details
+
+### Directory Structure (Target)
+```
+TinyTorch/
+├── modules/source/           # Student-facing modules
+├── instructor/              # Instructor resources
+│   ├── tools/              # Analysis and utility scripts
+│   ├── reports/            # Generated report cards
+│   ├── guides/             # Instructor documentation
+│   └── templates/          # Templates and examples
+├── docs/                   # Quarto documentation
+│   ├── _quarto.yml         # Quarto configuration
+│   ├── index.qmd           # Main documentation
+│   ├── modules/            # Module documentation
+│   └── instructor/         # Instructor documentation
+├── tests/                  # Test suites
+└── tinytorch/              # Main package
+```
+
+### Analysis Tools Organization
+- `instructor/tools/module_analyzer.py` - Main analysis tool
+- `instructor/tools/report_generator.py` - Report card generator
+- `instructor/tools/quality_monitor.py` - Continuous monitoring
+- `instructor/reports/` - Generated report cards by date
+- `instructor/guides/` - How-to guides for instructors
+
+### Documentation Strategy
+- **Quarto** for main documentation system
+- **Automated generation** from source code and analysis
+- **Multiple output formats** (HTML, PDF, etc.)
+- **Integrated report cards** in documentation
+- **Instructor and student** sections
+
+## 🎯 Success Metrics
+
+### Repository Organization
+- [ ] Clean, logical directory structure
+- [ ] All tools in appropriate locations
+- [ ] No broken imports or functionality
+- [ ] Easy to navigate and understand
+
+### Testing & Quality
+- [ ] 100% test pass rate across all modules
+- [ ] All analysis tools working correctly
+- [ ] No import errors or missing dependencies
+- [ ] Comprehensive test coverage
+
+### Report Cards
+- [ ] Professional, formatted report cards
+- [ ] Consistent design and layout
+- [ ] Clear, actionable insights
+- [ ] Easy to generate and update
+
+### Documentation
+- [ ] Quarto documentation system working
+- [ ] Professional manual-style documentation
+- [ ] Automated generation from source
+- [ ] Easy to maintain and update
+
+### Integration
+- [ ] All components work together seamlessly
+- [ ] Automated quality monitoring
+- [ ] Clear improvement tracking
+- [ ] Smooth development workflow
+
+## 🚀 Execution Timeline
+
+**Phase 1** (Branch 1): Repository structure reorganization
+**Phase 2** (Branch 2): Comprehensive testing and fixes
+**Phase 3** (Branch 3): Professional report card system
+**Phase 4** (Branch 4): Quarto documentation setup
+**Phase 5** (Branch 5): Integration and final polish
+
+Each phase will be completed in a separate branch, thoroughly tested, and merged only when fully verified.
+
+This plan ensures systematic improvement while maintaining quality and functionality throughout the process. 

instructor/tools/tinytorch_module_analyzer.py

@@ -80,7 +80,7 @@ class ModuleReportCard:
 class TinyTorchModuleAnalyzer:
     """Comprehensive analyzer for TinyTorch educational modules"""
     
-    def __init__(self, modules_dir: str = "modules/source"):
+    def __init__(self, modules_dir: str = "../../modules/source"):
         self.modules_dir = Path(modules_dir)
         self.target_metrics = {
             'ideal_lines': (200, 400),
@@ -913,7 +913,7 @@ def main():
     parser.add_argument("--compare", nargs="+", help="Compare multiple modules")
     parser.add_argument("--format", choices=["json", "html", "both"], default="both", help="Output format")
     parser.add_argument("--save", action="store_true", help="Save report cards to files")
-    parser.add_argument("--modules-dir", default="modules/source", help="Path to modules directory")
+    parser.add_argument("--modules-dir", default="../../modules/source", help="Path to modules directory")
     
     args = parser.parse_args()