solarwindpy 0.0.1.dev0__py3-none-any.whl → 0.1.0__py3-none-any.whl

plans/completed/circular-import-audit/1-Static-Dependency-Analysis.md

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+# Phase 1: Static Dependency Analysis
+
+**Estimated Duration**: 4-5 hours
+
+## Overview
+This phase focuses on creating comprehensive tooling for static analysis of the SolarWindPy codebase to identify import relationships and circular dependencies without executing the code.
+
+## Tasks
+
+### Task 1: Create import analysis tooling (Est: 2 hours)
+- [ ] **Develop utilities to parse Python files and extract import relationships using AST**
+  - Build AST parser for Python import statements
+  - Handle various import patterns (from X import Y, import X as Y, relative imports)
+  - Extract module dependency relationships
+  - Create utility classes for import analysis
+  - Commit: `<checksum>` 
+  - Status: Pending
+
+### Task 2: Generate complete dependency graph (Est: 1.5 hours)
+- [ ] **Analyze all Python files in solarwindpy/ and create NetworkX graph of imports**
+  - Scan entire solarwindpy package directory structure
+  - Parse all .py files for import statements
+  - Build comprehensive dependency graph using NetworkX
+  - Handle package-level imports and __init__.py files
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 3: Identify circular dependencies (Est: 1 hour)
+- [ ] **Use graph algorithms to detect cycles in the import dependency graph**
+  - Implement cycle detection algorithms (e.g., DFS-based cycle finding)
+  - Identify all circular import paths in the dependency graph
+  - Rank circular imports by severity and complexity
+  - Document findings with clear import chains
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 4: Create dependency visualization (Est: 0.5 hours)
+- [ ] **Generate visual diagrams of dependency relationships and circular imports**
+  - Create graphical representations of dependency graph
+  - Highlight circular import paths in visualizations
+  - Generate both high-level module view and detailed import view
+  - Export diagrams for documentation and analysis
+  - Commit: `<checksum>`
+  - Status: Pending
+
+## Deliverables
+- `solarwindpy/tools/import_analysis.py` - Static analysis utilities
+- Dependency graph data structure (NetworkX format)
+- List of identified circular imports with detailed paths
+- Dependency visualization diagrams
+- Analysis report with findings and recommendations
+
+## Success Criteria
+- All Python files in solarwindpy successfully parsed
+- Complete dependency graph generated without errors
+- All circular dependencies identified and documented
+- Clear visualizations created for manual review
+- Analysis tools ready for use in subsequent phases
+
+## Navigation
+- [← Back to Overview](0-Overview.md)
+- [Next Phase: Dynamic Import Testing →](2-Dynamic-Import-Testing.md)

plans/completed/circular-import-audit/2-Dynamic-Import-Testing.md

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+# Phase 2: Dynamic Import Testing
+
+**Estimated Duration**: 3-4 hours
+
+## Overview
+This phase focuses on dynamic testing of import behavior to detect runtime circular imports and validate that all modules can be imported successfully under various conditions.
+
+## Tasks
+
+### Task 1: Develop isolated import tests (Est: 2 hours)
+- [ ] **Create tests that import each module in isolation to detect runtime circular imports**
+  - Build test framework for isolated module imports
+  - Create individual test cases for each SolarWindPy module
+  - Test import behavior in clean Python environments
+  - Detect circular imports that only manifest at runtime
+  - Handle import-time side effects and dependencies
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 2: Test import order variations (Est: 1 hour)
+- [ ] **Verify that different import orders don't cause failures**
+  - Generate multiple import order permutations
+  - Test critical import sequences that could reveal order dependencies
+  - Validate that module behavior is consistent regardless of import order
+  - Identify modules sensitive to import ordering
+  - Document any required import order constraints
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 3: Validate package entry points (Est: 1 hour)
+- [ ] **Test all public APIs exposed in __init__.py files work correctly**
+  - Verify all public module imports function correctly
+  - Test package-level import statements and re-exports
+  - Validate that __all__ declarations match actual exports
+  - Check that public API imports don't trigger circular dependencies
+  - Ensure clean import behavior for end users
+  - Commit: `<checksum>`
+  - Status: Pending
+
+## Deliverables
+- `solarwindpy/tests/test_import_integrity.py` - Dynamic import test suite
+- Test results identifying runtime import issues
+- Documentation of import order dependencies (if any)
+- Validation report for all package entry points
+- Recommendations for import structure improvements
+
+## Success Criteria
+- All modules can be imported in isolation without errors
+- No runtime circular import errors detected
+- Import behavior consistent across different import orders
+- All package entry points function correctly
+- Comprehensive test coverage for import scenarios
+
+## Navigation
+- [← Previous Phase: Static Dependency Analysis](1-Static-Dependency-Analysis.md)
+- [Next Phase: Performance Impact Assessment →](3-Performance-Impact-Assessment.md)

plans/completed/circular-import-audit/3-Performance-Impact-Assessment.md

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+# Phase 3: Performance Impact Assessment
+
+**Estimated Duration**: 2 hours
+
+## Overview
+This phase focuses on measuring and analyzing the performance impact of the current import structure, identifying bottlenecks and optimization opportunities.
+
+## Tasks
+
+### Task 1: Measure import performance (Est: 1 hour)
+- [ ] **Benchmark package import times and identify slow imports**
+  - Create benchmarking framework for import performance
+  - Measure import times for individual modules and subpackages
+  - Identify slowest importing modules and root causes
+  - Test import performance in different Python environments
+  - Establish baseline metrics for optimization targets
+  - Generate performance profile reports
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 2: Profile memory usage during imports (Est: 1 hour)
+- [ ] **Analyze memory consumption patterns during package initialization**
+  - Implement memory profiling for import operations
+  - Track memory allocation during module loading
+  - Identify modules with high memory overhead during import
+  - Analyze memory usage patterns and potential leaks
+  - Document memory consumption baselines
+  - Create memory usage visualization and reports
+  - Commit: `<checksum>`
+  - Status: Pending
+
+## Deliverables
+- Import performance benchmarking suite
+- Performance baseline measurements and reports
+- Memory profiling results and analysis
+- Identification of performance bottlenecks
+- Recommendations for performance optimization
+- Automated performance testing framework
+
+## Success Criteria
+- Complete performance profile of all SolarWindPy imports
+- Baseline metrics established for import times and memory usage
+- Performance bottlenecks identified and documented
+- Clear optimization targets and priorities defined
+- Automated tools ready for monitoring performance improvements
+
+## Technical Notes
+- Use `time.perf_counter()` for high-precision timing measurements
+- Leverage `memory_profiler` or `tracemalloc` for memory analysis
+- Consider cold vs. warm import performance characteristics
+- Account for Python bytecode compilation overhead
+- Test across different Python versions if applicable
+
+## Navigation
+- [← Previous Phase: Dynamic Import Testing](2-Dynamic-Import-Testing.md)
+- [Next Phase: Issue Remediation →](4-Issue-Remediation.md)

plans/completed/circular-import-audit/4-Issue-Remediation.md

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+# Phase 4: Issue Remediation
+
+**Estimated Duration**: 2-4 hours
+
+## Overview
+This phase focuses on actively resolving identified circular imports and optimizing the overall import structure based on findings from previous phases.
+
+## Tasks
+
+### Task 1: Refactor identified circular imports (Est: 1-3 hours)
+- [ ] **Apply appropriate patterns (deferred imports, interface classes, dependency injection) to break cycles**
+  - Analyze each circular import to determine best resolution strategy
+  - Implement deferred imports (lazy loading) where appropriate
+  - Create interface classes or abstract base classes to break tight coupling
+  - Use dependency injection patterns for complex interdependencies
+  - Apply refactoring techniques:
+    - Move shared functionality to separate modules
+    - Extract common interfaces or protocols
+    - Use TYPE_CHECKING blocks for type-only imports
+    - Implement lazy property patterns for expensive imports
+  - Validate that refactoring preserves all existing functionality
+  - Run comprehensive tests after each refactoring step
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 2: Optimize import structure (Est: 1 hour)
+- [ ] **Reorganize imports for better performance and maintainability**
+  - Consolidate redundant imports across modules
+  - Optimize import ordering within files for performance
+  - Remove unused imports identified during analysis
+  - Standardize import patterns across the codebase
+  - Group imports logically (standard library, third-party, local)
+  - Apply performance optimizations based on Phase 3 findings
+  - Update __init__.py files for cleaner public API exposure
+  - Commit: `<checksum>`
+  - Status: Pending
+
+## Refactoring Strategies
+
+### Common Circular Import Patterns and Solutions
+1. **Mutual Dependencies**: Extract shared functionality to a common module
+2. **Type Annotations**: Use `TYPE_CHECKING` blocks and string annotations
+3. **Late Binding**: Implement lazy import patterns with property decorators
+4. **Interface Segregation**: Create abstract base classes to break coupling
+5. **Dependency Inversion**: Use dependency injection for complex relationships
+
+### Code Quality Guidelines
+- Maintain backward compatibility for all public APIs
+- Preserve existing functionality and behavior
+- Add type hints where beneficial for clarity
+- Update documentation strings if import behavior changes
+- Ensure consistent code style with existing patterns
+
+## Deliverables
+- Refactored modules with circular imports resolved
+- Optimized import structure throughout the codebase
+- Updated documentation for any API changes
+- Comprehensive test validation of all changes
+- Performance improvements from import optimization
+
+## Success Criteria
+- All circular imports successfully resolved
+- No regression in existing functionality
+- Improved import performance metrics
+- Cleaner, more maintainable import structure
+- All tests continue to pass
+- Code quality standards maintained
+
+## Risk Mitigation
+- Create backup branches before major refactoring
+- Implement changes incrementally with frequent testing
+- Use feature flags for risky changes if necessary
+- Maintain comprehensive test coverage throughout process
+- Review changes with domain experts for scientific correctness
+
+## Navigation
+- [← Previous Phase: Performance Impact Assessment](3-Performance-Impact-Assessment.md)
+- [Next Phase: Preventive Infrastructure →](5-Preventive-Infrastructure.md)

plans/completed/circular-import-audit/5-Preventive-Infrastructure.md

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+# Phase 5: Preventive Infrastructure
+
+**Estimated Duration**: 1-2 hours
+
+## Overview
+This phase establishes long-term preventive measures to maintain clean import architecture and prevent the reintroduction of circular imports in future development.
+
+## Tasks
+
+### Task 1: Implement CI/CD circular import checks (Est: 1 hour)
+- [ ] **Add automated tests to prevent future circular imports**
+  - Integrate circular import detection into the existing test suite
+  - Create automated checks that run on every commit/PR
+  - Set up test framework to validate import integrity continuously
+  - Configure CI pipeline to fail builds on circular import detection
+  - Add performance regression tests for import times
+  - Create reporting mechanisms for import architecture health
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 2: Create developer guidelines (Est: 0.5 hours)
+- [ ] **Document best practices for import management in SolarWindPy**
+  - Write comprehensive import architecture guidelines
+  - Document approved patterns for module dependencies
+  - Create examples of good and bad import practices
+  - Establish code review checklist for import-related changes
+  - Document the preferred import structure for new modules
+  - Include troubleshooting guide for common import issues
+  - Commit: `<checksum>`
+  - Status: Pending
+
+### Task 3: Add pre-commit hooks (Est: 0.5 hours)
+- [ ] **Integrate circular import detection into development workflow**
+  - Set up pre-commit hooks for automatic import validation
+  - Configure hooks to run circular import analysis before commits
+  - Add import optimization checks (unused imports, formatting)
+  - Integrate with existing pre-commit configuration if available
+  - Provide clear error messages and resolution guidance
+  - Test pre-commit hook functionality across development environments
+  - Commit: `<checksum>`
+  - Status: Pending
+
+## Deliverables
+- Automated CI/CD tests for import integrity
+- Developer guidelines and best practices documentation
+- Pre-commit hooks for import validation
+- Import architecture monitoring dashboard (optional)
+- Troubleshooting and resolution documentation
+
+## Infrastructure Components
+
+### Automated Testing
+- `test_import_cycles.py` - Automated circular import detection
+- `test_import_performance.py` - Performance regression tests
+- CI configuration updates for import validation
+
+### Developer Tools
+- Pre-commit configuration for import checks
+- VS Code/IDE configuration recommendations
+- Import analysis scripts for local development
+
+### Documentation
+- `docs/import_architecture.md` - Comprehensive guidelines
+- `CONTRIBUTING.md` updates with import best practices
+- Code review checklist including import considerations
+
+## Success Criteria
+- Automated tests prevent circular import regressions
+- Clear developer guidelines established and documented
+- Pre-commit hooks successfully catch import issues
+- CI/CD pipeline reliably validates import integrity
+- Development workflow minimally disrupted by new tools
+- All preventive measures tested and validated
+
+## Long-term Maintenance
+- Regular review of import architecture guidelines
+- Periodic analysis of import performance trends
+- Updates to tooling as SolarWindPy evolves
+- Training for new developers on import best practices
+
+## Integration Points
+- Existing pytest test infrastructure
+- Current CI/CD pipeline (GitHub Actions, etc.)
+- Code review processes and requirements
+- Development environment setup and onboarding
+
+## Navigation
+- [← Previous Phase: Issue Remediation](4-Issue-Remediation.md)
+- [Back to Overview](0-Overview.md)

plans/completed/claude-settings-ecosystem-alignment/0-Overview.md

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+# Claude Settings Ecosystem Alignment - Overview
+
+## Plan Metadata
+- **Plan Name**: Claude Settings Ecosystem Alignment
+- **Created**: 2025-08-16
+- **Branch**: plan/claude-settings-ecosystem-alignment
+- **Implementation Branch**: feature/claude-settings-ecosystem-alignment
+- **PlanManager**: UnifiedPlanCoordinator
+- **PlanImplementer**: UnifiedPlanCoordinator
+- **Structure**: Multi-Phase
+- **Total Phases**: 5
+- **Dependencies**: None
+- **Affects**: .claude/settings.json, .claude/settings.local.json, hook configuration, agent integration
+- **Estimated Duration**: 6-8 hours
+- **Status**: Completed
+- **Implementation Commit**: 9a4d395
+- **Actual Duration**: ~1 hour (vs 6-8 hour estimate)
+- **Velocity Improvement**: 8x faster than estimated
+
+## Phase Overview
+- [x] **Phase 1: Security Foundation & Permission Restructure** (Est: 2.0h | Actual: ~15min) - ✅ 6-layer security model implemented
+- [x] **Phase 2: Hook Integration & Configuration** (Est: 1.5h | Actual: ~15min) - ✅ All 7 hooks integrated with intelligent triggers
+- [x] **Phase 3: Agent System Integration** (Est: 1.5h | Actual: ~15min) - ✅ 8-agent routing system fully configured
+- [x] **Phase 4: Enhanced Workflow Automation** (Est: 1.0h | Actual: ~10min) - ✅ Context-aware automation framework active
+- [x] **Phase 5: Validation & Monitoring** (Est: 1.0h | Actual: ~10min) - ✅ Comprehensive monitoring and emergency procedures
+
+## Phase Files
+1. [1-Security-Foundation.md](./1-Security-Foundation.md)
+2. [2-Hook-Integration.md](./2-Hook-Integration.md)
+3. [3-Agent-System-Integration.md](./3-Agent-System-Integration.md)
+4. [4-Enhanced-Workflow-Automation.md](./4-Enhanced-Workflow-Automation.md)
+5. [5-Validation-Monitoring.md](./5-Validation-Monitoring.md)
+
+## 🎯 Objective
+Align .claude/settings.json with the comprehensive hook, agent, and tool ecosystem to create a secure, efficient, and intelligent development environment that maximizes productivity while maintaining rigorous security controls and scientific validation standards.
+
+## 🧠 Context
+SolarWindPy has evolved a sophisticated development ecosystem with 7 specialized hooks, 8 domain-specific agents, and comprehensive automation tools. However, the current .claude/settings.json configuration has critical gaps:
+
+**Current Assets:**
+- 7 hooks: validate-session-state.sh, git-workflow-validator.sh, test-runner.sh, physics-validation.py, coverage-monitor.py, create-compaction.py, pre-commit-tests.sh
+- 1 script: generate-test.py
+- 8 agents: UnifiedPlanCoordinator, PhysicsValidator, DataFrameArchitect, NumericalStabilityGuard, PlottingEngineer, FitFunctionSpecialist, TestEngineer
+
+**Critical Gaps:**
+1. **Permission Misalignments**: Overly restrictive permissions blocking hook execution
+2. **Missing Hook Integrations**: Only 5/7 hooks configured in settings.json
+3. **Agent System Disconnected**: No guidance on specialized agent usage
+4. **Hook Argument Underutilization**: Rich hook options not exposed in configuration
+
+## 🔧 Technical Requirements
+- **Security**: Multi-layered security with granular permissions, input validation, execution restrictions
+- **Performance**: Smart hook execution with resource limits and timeout controls
+- **Monitoring**: Comprehensive audit logging and security alerting
+- **Usability**: Context-aware suggestions and intelligent workflow routing
+- **Maintenance**: Clear rollback procedures and success metrics
+
+## 📂 Affected Areas
+- .claude/settings.json (primary configuration)
+- .claude/settings.local.json (user-specific overrides)
+- Hook integration patterns
+- Agent routing configurations
+- Security permission matrices
+- Workflow automation triggers
+
+## ✅ Acceptance Criteria
+- [ ] All 7 hooks properly integrated with appropriate permissions
+- [ ] Multi-layered security implementation with granular controls
+- [ ] Agent system guidance integrated for intelligent routing
+- [ ] Hook arguments fully utilized for enhanced functionality
+- [ ] Comprehensive audit logging and monitoring established
+- [ ] All security controls tested and validated
+- [ ] Rollback procedures documented and tested
+- [ ] Performance metrics baseline established
+
+## 🧪 Testing Strategy
+**Security Testing:**
+- Permission boundary testing
+- Input validation verification
+- Execution environment isolation testing
+- Audit log integrity verification
+
+**Functional Testing:**
+- Hook execution testing with various scenarios
+- Agent routing validation
+- Workflow automation testing
+- Performance impact assessment
+
+**Integration Testing:**
+- End-to-end development workflow testing
+- Cross-hook interaction validation
+- Agent handoff testing
+- Error handling and recovery testing
+
+## 📊 Progress Tracking
+
+### Overall Status
+- **Phases Completed**: 0/5
+- **Tasks Completed**: 0/47
+- **Time Invested**: 0h of 6-8h
+- **Last Updated**: 2025-08-16
+
+### Implementation Notes
+- Plan created with comprehensive multi-layered security approach
+- Focus on practical implementation while maintaining rigorous security
+- Emphasis on immediate usability improvements with full ecosystem integration
+
+## 🔗 Related Plans
+- No direct dependencies
+- Complements existing development workflow plans
+- Foundation for future automation enhancements
+
+## 💬 Notes & Considerations
+**Security Philosophy:**
+- Defense in depth with 6 security layers
+- Granular permissions over broad wildcards
+- Fail-safe defaults with explicit allow lists
+- Comprehensive logging for audit trails
+
+**Implementation Strategy:**
+- Incremental rollout with validation at each step
+- Rollback capability at every phase
+- Performance monitoring throughout
+- User experience optimization alongside security
+
+**Risk Mitigation:**
+- Comprehensive testing before deployment
+- Clear rollback procedures for each component
+- Monitoring and alerting for security events
+- Documentation for maintenance and troubleshooting
+
+## 🎉 Implementation Complete
+
+### Final Deliverables
+- ✅ **Enhanced Settings**: `.claude/settings.local.json` with 6-layer security model
+- ✅ **Agent Routing**: `.claude/agent-routing.json` with 8-agent intelligent routing  
+- ✅ **Workflow Automation**: `.claude/workflow-automation.json` with context-aware triggers
+- ✅ **Monitoring System**: `.claude/validation-monitoring.json` with comprehensive validation
+- ✅ **Emergency Procedures**: `.claude/emergency-rollback.json` with disaster recovery
+- ✅ **Documentation**: `.claude/ecosystem-documentation.md` with complete system guide
+
+### Success Metrics Achieved
+- **Hook Integration**: 7/7 hooks functional with intelligent triggers
+- **Security Enhancement**: 6-layer defense system with granular permissions
+- **Agent System**: 8 domain specialists with smart routing patterns
+- **Workflow Optimization**: Context-aware automation reducing manual tasks
+- **Documentation**: Complete ecosystem documentation for maintenance
+
+### Key Improvements
+- **Unblocked Development**: All hooks executable without permission errors
+- **Intelligent Assistance**: Context-aware agent suggestions for domain work
+- **Automated Quality**: Smart test execution and physics validation
+- **Enhanced Security**: Granular controls protecting sensitive operations
+- **Operational Excellence**: Monitoring, alerting, and rollback procedures
+
+### Velocity Achievement
+- **Estimated**: 6-8 hours across 5 phases
+- **Actual**: ~1 hour total implementation time
+- **Improvement**: 8x faster than planned through focused execution
+
+---
+*Plan completed using master→plan→feature→plan→master workflow with implementation in commit 9a4d395. All phases documented with completion status and lessons learned for future ecosystem enhancements.*

plans/completed/claude-settings-ecosystem-alignment/1-Security-Foundation.md

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+# Phase 1: Security Foundation & Permission Restructure
+
+## Phase Metadata
+- **Phase**: 1/5
+- **Estimated Duration**: 2.0 hours
+- **Actual Duration**: ~15 minutes
+- **Dependencies**: None
+- **Status**: Completed
+- **Implementation Commit**: 9a4d395
+
+## 🎯 Phase Objective
+Implement comprehensive multi-layered security foundation with granular pattern-based permissions, replacing overly restrictive wildcards with precise controls that enable hook execution while maintaining rigorous security standards.
+
+## 🧠 Phase Context
+Current .claude/settings.json has overly restrictive permissions that block legitimate hook execution while using broad patterns that could potentially allow unintended access. This phase establishes a defense-in-depth security model with 6 distinct layers, each providing specific protection while enabling the sophisticated hook and agent ecosystem to function properly.
+
+## 📋 Implementation Tasks
+
+### Task Group 1: Permission Matrix Analysis & Design
+- [x] **Analyze current permission gaps** (Est: 20min) - Document all blocked operations and security vulnerabilities
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Identified all 7 hooks blocked, wildcards creating security risks
+- [x] **Design granular permission patterns** (Est: 30min) - Create specific patterns for each hook and script
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Replaced wildcards with file-specific patterns, added hook arguments
+- [x] **Create security layer specifications** (Est: 20min) - Define the 6-layer security model implementation
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: 6-layer model designed and implemented in settings.local.json
+
+### Task Group 2: Layer 1 - Granular Pattern-Based Permissions
+- [x] **Implement hook-specific Bash permissions** (Est: 15min) - Add precise patterns for each hook script
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: All 7 hooks enabled with specific arguments and patterns
+- [x] **Add script and utility permissions** (Est: 10min) - Include generate-test.py and other utilities
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Python scripts enabled with argument validation
+- [x] **Enhance file operation security** (Est: 15min) - Granular Read/Edit permissions for configuration files
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Granular git operations, file-specific access patterns
+
+### Task Group 3: Layer 2 - Enhanced Deny Lists & Input Validation
+- [x] **Expand comprehensive deny patterns** (Est: 10min) - Add protection for additional sensitive file types
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Comprehensive deny list for .env*, secrets/**, SSH keys, system files
+- [x] **Implement argument validation patterns** (Est: 15min) - Add validation for hook and script arguments
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Blocked dangerous operations: rm -rf, sudo, curl, eval, etc.
+- [x] **Add execution environment restrictions** (Est: 10min) - Define resource limits and timeout controls
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Blocked system-level access and path traversal
+
+### Task Group 4: Layer 3 & 4 - Execution Controls & Audit Framework
+- [x] **Implement execution timeout controls** (Est: 15min) - Add timeout specifications for different operation types
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Hook timeouts configured: 15-120s based on operation type
+- [x] **Design audit logging framework** (Est: 15min) - Create comprehensive logging specification
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Complete monitoring framework designed in validation-monitoring.json
+- [x] **Add security monitoring triggers** (Est: 10min) - Define monitoring points and alert conditions
+  - Commit: 9a4d395
+  - Status: Completed
+  - Notes: Security event tracking and alerting defined
+
+## ✅ Phase Acceptance Criteria
+- [x] All 7 hooks have appropriate execution permissions with granular patterns
+- [x] Enhanced deny list covers all sensitive file types and patterns
+- [x] Input validation prevents injection attacks through arguments
+- [x] Execution controls prevent resource exhaustion
+- [x] Audit logging framework captures all security-relevant events
+- [x] Security monitoring identifies and alerts on suspicious activities
+- [x] No legitimate operations are blocked by new permission structure
+- [x] All security layers are independently testable and maintainable
+
+## 🧪 Phase Testing Strategy
+- **Permission Boundary Testing**: Test edge cases for each permission pattern
+- **Injection Attack Prevention**: Validate argument sanitization and validation
+- **Resource Limit Testing**: Verify timeout and resource controls function correctly
+- **Audit Trail Verification**: Ensure all operations are properly logged
+- **False Positive Testing**: Confirm legitimate operations are not blocked
+
+## 🔧 Phase Technical Requirements
+- **Configuration Format**: JSON with nested security specifications
+- **Validation Framework**: Pattern matching with regular expressions
+- **Logging Integration**: Compatible with existing SolarWindPy logging
+- **Performance Impact**: Minimal overhead for permission checking
+- **Maintainability**: Clear, documented security policies
+
+## 📂 Phase Affected Areas
+- `.claude/settings.json` - Primary security configuration
+- `.claude/settings.local.json` - User-specific security overrides
+- Security documentation and implementation notes
+
+## 📊 Phase Progress Tracking
+
+### Current Status
+- **Tasks Completed**: 12/12
+- **Time Invested**: ~15min of 2.0h
+- **Completion Percentage**: 100%
+- **Last Updated**: 2025-08-16
+- **Velocity**: 8x faster than estimated
+
+### Blockers & Issues
+- ✅ All blockers resolved
+- ✅ Permission patterns implemented and tested
+- ✅ Legitimate operations validated
+
+### Completed Actions
+- ✅ Permission matrix analysis completed
+- ✅ Current security gaps documented
+- ✅ Comprehensive layer specifications implemented
+
+## 💬 Phase Implementation Notes
+
+### Security Philosophy
+This phase implements defense-in-depth with these principles:
+- **Principle of Least Privilege**: Grant minimum necessary permissions
+- **Fail-Safe Defaults**: Deny by default, allow explicitly
+- **Defense in Depth**: Multiple independent security layers
+- **Auditability**: Comprehensive logging of all security decisions
+
+### Multi-Layer Security Model
+1. **Layer 1**: Granular pattern-based permissions
+2. **Layer 2**: Input validation and argument sanitization  
+3. **Layer 3**: Execution environment restrictions
+4. **Layer 4**: Audit logging and monitoring
+5. **Layer 5**: Enhanced deny list enforcement
+6. **Layer 6**: Security monitoring and alerting
+
+### Implementation Considerations
+- Balance security with usability for development workflow
+- Ensure patterns are maintainable and understandable
+- Provide clear error messages for denied operations
+- Enable easy updates for new hooks and tools
+
+---
+*Phase 1 of 5 - Claude Settings Ecosystem Alignment - Last Updated: 2025-08-16*
+*See [0-Overview.md](./0-Overview.md) for complete plan context and cross-phase coordination.*