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+# Code Quality Analyzer Reference
+
+Comprehensive reference guides for code quality analysis, security review, clarity refactoring, and architectural patterns.
+
+## Files in This Directory
+
+### [security-checklist.md](security-checklist.md)
+Complete security checklist covering OWASP Top 10, input validation, authentication, cryptography, and data protection with actionable checks.
+
+**When to use**: Security reviews, pre-deployment audits, vulnerability assessments
+**Coverage**: OWASP Top 10, CWE database, common vulnerabilities
+
+### [clarity-refactoring-rules.md](clarity-refactoring-rules.md)
+10 proven refactoring rules for improving code clarity, reducing complexity, and eliminating technical debt without changing behavior.
+
+**When to use**: Code reviews, refactoring sessions, complexity reduction
+**Key topics**: Guard clauses, extract functions, explaining variables, naming conventions
+
+### [code-quality-metrics.md](code-quality-metrics.md)
+Understanding and interpreting code quality metrics including cyclomatic complexity, maintainability index, code duplication, and test coverage.
+
+**When to use**: Quality assessments, setting standards, tracking improvements
+**Metrics**: Complexity, duplication, coverage, maintainability scores
+
+### [architecture-patterns.md](architecture-patterns.md)
+Best practices for clean architecture, layering, dependency management, and preventing architectural erosion in multi-module codebases.
+
+**When to use**: Synthesis analysis, architectural reviews, system design
+**Patterns**: Layered architecture, dependency injection, circular dependency prevention
+
+### [analysis-workflows.md](analysis-workflows.md)
+Step-by-step workflows for conducting security reviews, clarity refactorings, and synthesis analysis with practical timelines and checklists.
+
+**When to use**: Planning code quality initiatives, conducting audits
+**Workflows**: Security review process, refactoring workflow, synthesis analysis
+
+## Quick Reference
+
+### Security Review Process
+1. Run automated scanners (Bandit, Semgrep)
+2. Manual code review for OWASP Top 10
+3. Generate security scorecard
+4. Prioritize by severity (Critical → High → Medium)
+5. Fix and verify
+6. Re-scan to confirm
+
+### Clarity Refactoring Process
+1. Identify complexity hotspots (complexity > 10)
+2. Apply guard clauses to flatten nesting
+3. Extract functions for single responsibility
+4. Add explaining variables for complex logic
+5. Replace magic numbers with constants
+6. Measure before/after complexity
+
+### Synthesis Analysis Process
+1. Map module dependencies
+2. Identify circular dependencies
+3. Detect architectural violations
+4. Find code duplication across files
+5. Check consistency (naming, errors, patterns)
+6. Enforce architectural standards
+
+## Navigation by Use Case
+
+**I need to**... | **Use this guide**...
+---|---
+Fix security vulnerabilities | [security-checklist.md](security-checklist.md)
+Reduce code complexity | [clarity-refactoring-rules.md](clarity-refactoring-rules.md)
+Understand quality metrics | [code-quality-metrics.md](code-quality-metrics.md)
+Enforce clean architecture | [architecture-patterns.md](architecture-patterns.md)
+Plan a code quality audit | [analysis-workflows.md](analysis-workflows.md)
+
+---
+
+Return to [agent documentation](../code-quality-analyzer.md)