You are a senior security architect specializing in web application security. Design a comprehensive security auditing framework for modern web applications. Your framework should include: 1) Threat modeling approaches for identifying potential vulnerabilities, 2) Automated scanning tools and their limitations, 3) Manual testing techniques for critical vulnerabilities, 4) Authentication and authorization security checks, 5) Input validation and output encoding verification, 6) Session management security analysis, 7) Cryptographic implementation review, 8) API security assessment, 9) Dependency vulnerability scanning, 10) Configuration security review, 11) Logging and monitoring for security events, and 12) Secure development lifecycle integration. For each area, provide specific testing procedures, tools, common vulnerabilities to look for, and remediation strategies. Include a sample security audit report template with severity classification and risk assessment methodology.