diff --git a/shellgenius/refactoring.py b/shellgenius/refactoring.py
new file mode 100644
index 0000000..8151f68
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+++ b/shellgenius/refactoring.py
@@ -0,0 +1,408 @@
+"""Refactoring analyzer module for ShellGenius."""
+
+import re
+from dataclasses import dataclass
+from typing import Any, Dict, List, Optional
+
+from shellgenius.config import get_config
+from shellgenius.generation import ShellParser, get_ollama_client
+
+
+@dataclass
+class RefactoringIssue:
+    """A refactoring issue found in a script."""
+
+    line_number: int
+    original: str
+    issue_type: str
+    severity: str
+    description: str
+    risk_assessment: str
+    suggestion: str
+    safer_alternative: str
+
+
+@dataclass
+class RefactoringResult:
+    """Complete refactoring analysis result."""
+
+    shell_type: str
+    issues: List[RefactoringIssue]
+    score: int
+    suggestions: List[str]
+    safer_script: str
+
+
+class SecurityRulesDB:
+    """Database of security rules for shell scripts."""
+
+    RULES = [
+        {
+            "id": "CWE-78",
+            "name": "Shell Injection",
+            "pattern": r"(rm|mv|cp|chmod|chown)\s+.*\$",
+            "severity": "high",
+            "description": "Command injection via variable expansion",
+            "risk": "Could execute unintended commands if variable contains shell metacharacters",
+            "alternative": "Use quotes around variables: \"$var\" instead of $var",
+        },
+        {
+            "id": "CWE-22",
+            "name": "Path Traversal",
+            "pattern": r"(cat|less|more|head|tail|rm|cp)\s+.*\.\./",
+            "severity": "medium",
+            "description": "Path traversal via ..",
+            "risk": "Could access files outside intended directory",
+            "alternative": "Use realpath() to resolve paths or validate input",
+        },
+        {
+            "id": "CWE-377",
+            "name": "Insecure Temporary File",
+            "pattern": r"(cat|mkdir|touch)\s+.*\/tmp\/[^\s]+",
+            "severity": "medium",
+            "description": "Insecure temporary file usage",
+            "risk": "Race condition vulnerability (TOCTOU)",
+            "alternative": "Use mktemp or dedicated temp directory functions",
+        },
+        {
+            "id": "CWE-退",
+            "name": "Eval with User Input",
+            "pattern": r"\beval\s+\$",
+            "severity": "critical",
+            "description": "Eval with variable input",
+            "risk": "Shell injection vulnerability",
+            "alternative": "Avoid eval, use direct variable references",
+        },
+        {
+            "id": "CWE-294",
+            "name": "Insecure File Permissions",
+            "pattern": r"chmod\s+777",
+            "severity": "high",
+            "description": "World-writable permissions",
+            "risk": "Security vulnerability - any user can modify",
+            "alternative": "Use chmod 755 for directories, 644 for files",
+        },
+        {
+            "id": "CWE-362",
+            "name": "Race Condition",
+            "pattern": r"(if|while)\s+.*-f\s+\$",
+            "severity": "medium",
+            "description": "TOCTOU race condition",
+            "risk": "File may change between check and use",
+            "alternative": "Use set -C (noclobber) or atomic operations",
+        },
+        {
+            "id": "CWE-323",
+            "name": "Reusing UID/GID",
+            "pattern": r"useradd\s+[^-]",
+            "severity": "low",
+            "description": "User creation without system considerations",
+            "risk": "UID/GID conflicts possible",
+            "alternative": "Use useradd -M -r or adduser system tools",
+        },
+    ]
+
+    @classmethod
+    def get_rules(cls) -> List[Dict[str, Any]]:
+        """Get all security rules.
+
+        Returns:
+            List of rule dictionaries
+        """
+        return cls.RULES
+
+    @classmethod
+    def check_rule(cls, line: str) -> Optional[Dict[str, Any]]:
+        """Check if line matches a security rule.
+
+        Args:
+            line: Shell command line
+
+        Returns:
+            Matching rule or None
+        """
+        for rule in cls.RULES:
+            if re.search(rule["pattern"], line, re.IGNORECASE):
+                return rule
+        return None
+
+
+class RefactoringAnalyzer:
+    """Shell script refactoring and security analyzer."""
+
+    BEST_PRACTICES = [
+        "Use set -euo pipefail for error handling",
+        "Quote all variable expansions: \"$var\"",
+        "Use functions for code organization",
+        "Add shebang for portability",
+        "Use absolute paths when possible",
+        "Implement proper error handling",
+        "Avoid magic numbers, use variables",
+        "Add comments for complex logic",
+    ]
+
+    IMPROVEMENTS = [
+        "Replace backticks with $() for command substitution",
+        "Use [[ ]] instead of [ ] for conditionals",
+        "Replace deprecated syntax with modern alternatives",
+        "Add error handling with set -e or trap",
+        "Use readonly for constants",
+        "Use local variables in functions",
+        "Avoid using exit codes incorrectly",
+    ]
+
+    def __init__(self):
+        """Initialize analyzer."""
+        self.parser = ShellParser()
+        self.client = get_ollama_client()
+        self.rules_db = SecurityRulesDB()
+
+    def analyze(
+        self, script: str, include_suggestions: bool = True
+    ) -> RefactoringResult:
+        """Analyze script for refactoring opportunities.
+
+        Args:
+            script: Shell script content
+            include_ai_suggestions: Include AI-generated suggestions
+
+        Returns:
+            RefactoringResult with issues and suggestions
+        """
+        shell_type = self.parser.detect_shell(script)
+        issues = self._find_issues(script)
+        score = self._calculate_score(issues, script)
+
+        suggestions = self._generate_suggestions(issues, script)
+
+        if include_suggestions:
+            ai_suggestions = self._get_ai_suggestions(script, shell_type)
+            suggestions.extend(ai_suggestions)
+
+        safer_script = self._generate_safer_script(script, issues)
+
+        return RefactoringResult(
+            shell_type=shell_type,
+            issues=issues,
+            score=score,
+            suggestions=suggestions,
+            safer_script=safer_script,
+        )
+
+    def _find_issues(self, script: str) -> List[RefactoringIssue]:
+        """Find issues in script.
+
+        Args:
+            script: Shell script content
+
+        Returns:
+            List of RefactoringIssue
+        """
+        issues = []
+        lines = script.split("\n")
+
+        for i, line in enumerate(lines, 1):
+            stripped = line.strip()
+            if not stripped or stripped.startswith("#"):
+                continue
+
+            rule = self.rules_db.check_rule(stripped)
+            if rule:
+                issues.append(
+                    RefactoringIssue(
+                        line_number=i,
+                        original=stripped,
+                        issue_type=rule["name"],
+                        severity=rule["severity"],
+                        description=rule["description"],
+                        risk_assessment=rule["risk"],
+                        suggestion=f"See alternative for {rule['name']}",
+                        safer_alternative=rule["alternative"],
+                    )
+                )
+            else:
+                improvement = self._check_improvements(stripped)
+                if improvement:
+                    issues.append(
+                        RefactoringIssue(
+                            line_number=i,
+                            original=stripped,
+                            issue_type="Code Quality",
+                            severity="low",
+                            description=improvement["description"],
+                            risk_assessment=improvement["risk"],
+                            suggestion=improvement["suggestion"],
+                            safer_alternative=improvement["alternative"],
+                        )
+                    )
+
+        return issues
+
+    def _check_improvements(
+        self, line: str
+    ) -> Optional[Dict[str, str]]:
+        """Check for code quality improvements.
+
+        Args:
+            line: Shell command line
+
+        Returns:
+            Improvement suggestion or None
+        """
+        if re.search(r"`[^`]+`", line):
+            return {
+                "description": "Use of backticks for command substitution",
+                "risk": "Backticks are deprecated and hard to nest",
+                "suggestion": "Use $() syntax instead",
+                "alternative": re.sub(r"`([^`]+)`", r"$(\1)", line),
+            }
+        if re.search(r"\[\s*[\^\]]+\]", line) and "=" in line:
+            return {
+                "description": "Use of [ ] instead of [[ ]]",
+                "risk": "[ ] has limitations with pattern matching",
+                "suggestion": "Use [[ ]] for modern bash",
+                "alternative": line.replace("[ ", "[[ ").replace(" ]", " ]]"),
+            }
+        return None
+
+    def _calculate_score(
+        self, issues: List[RefactoringIssue], script: str
+    ) -> int:
+        """Calculate overall script score.
+
+        Args:
+            issues: List of found issues
+            script: Original script
+
+        Returns:
+            Score from 0-100
+        """
+        base_score = 100
+        severity_weights = {"critical": 25, "high": 15, "medium": 10, "low": 5}
+
+        for issue in issues:
+            base_score -= severity_weights.get(issue.severity, 5)
+
+        lines_count = len([l for l in script.split("\n") if l.strip()])
+        if lines_count > 0 and base_score > 50:
+            density_bonus = min(10, lines_count // 20)
+            base_score += density_bonus
+
+        return max(0, min(100, base_score))
+
+    def _generate_suggestions(
+        self, issues: List[RefactoringIssue], script: str
+    ) -> List[str]:
+        """Generate list of improvement suggestions.
+
+        Args:
+            issues: List of found issues
+            script: Original script
+
+        Returns:
+            List of suggestion strings
+        """
+        suggestions = []
+
+        if not script.strip().startswith("#!"):
+            suggestions.append("Add shebang (#!/bin/bash) for portability")
+
+        if "set -" not in script:
+            suggestions.append(
+                "Add 'set -euo pipefail' for better error handling"
+            )
+
+        if issues:
+            severity_counts = {}
+            for issue in issues:
+                severity_counts[issue.severity] = (
+                    severity_counts.get(issue.severity, 0) + 1
+                )
+            for severity, count in sorted(
+                severity_counts.items(), key=lambda x: x[0]
+            ):
+                suggestions.append(
+                    f"Address {count} {severity} severity issue(s)"
+                )
+
+        suggestions.extend(
+            self.BEST_PRACTICES[:3]
+        )
+
+        return suggestions
+
+    def _get_ai_suggestions(
+        self, script: str, shell_type: str
+    ) -> List[str]:
+        """Get AI-generated improvement suggestions.
+
+        Args:
+            script: Shell script content
+            shell_type: Shell type
+
+        Returns:
+            List of suggestion strings
+        """
+        from shellgenius.generation import PromptTemplates
+
+        prompt = PromptTemplates.get_refactor_prompt(script, shell_type)
+        result = self.client.generate(prompt)
+
+        if result["success"]:
+            response = result["response"].get("response", "")
+            return [line.strip() for line in response.split("\n") if line.strip()]
+        return []
+
+    def _generate_safer_script(
+        self, script: str, issues: List[RefactoringIssue]
+    ) -> str:
+        """Generate safer version of script.
+
+        Args:
+            script: Original script
+            issues: List of issues to fix
+
+        Returns:
+            Safer version of script
+        """
+        lines = script.split("\n")
+        fixed_lines = []
+        issue_map = {i.issue_type: i for i in issues}
+
+        for i, line in enumerate(lines, 1):
+            stripped = line.strip()
+            if not stripped:
+                fixed_lines.append(line)
+                continue
+
+            fixed = stripped
+            for issue in issues:
+                if issue.line_number == i and issue.safer_alternative:
+                    if issue.safer_alternative not in ["", stripped]:
+                        fixed = issue.safer_alternative
+                        break
+
+            if not stripped.startswith("#!") and i == 1:
+                fixed_lines.append("#!/bin/bash")
+                fixed_lines.append("set -euo pipefail")
+                fixed_lines.append("")
+
+            fixed_lines.append(fixed if fixed else line)
+
+        return "\n".join(fixed_lines)
+
+
+def refactor_script(
+    script: str, include_suggestions: bool = True
+) -> RefactoringResult:
+    """Convenience function to analyze and refactor a shell script.
+
+    Args:
+        script: Shell script content
+        include_suggestions: Include AI suggestions
+
+    Returns:
+        RefactoringResult
+    """
+    analyzer = RefactoringAnalyzer()
+    return analyzer.analyze(script, include_suggestions)