diff --git a/src/generators/merge.py b/src/generators/merge.py
new file mode 100644
index 0000000..52e9a09
--- /dev/null
+++ b/src/generators/merge.py
@@ -0,0 +1,264 @@
+"""Pattern merging logic for handling multiple stacks."""
+
+from typing import Dict, List, Optional, Set, Tuple
+
+
+class PatternMerger:
+    """Merges patterns from multiple sources with deduplication and conflict resolution."""
+
+    def __init__(self) -> None:
+        self.priority_weights = {
+            "os": 10,
+            "ide": 20,
+            "language": 30,
+            "framework": 40,
+            "custom": 50,
+        }
+
+    def merge(
+        self,
+        patterns_by_category: Dict[str, List[str]],
+        custom_patterns: Optional[List[str]] = None,
+        strategy: str = "priority",
+    ) -> Tuple[List[str], List[str]]:
+        """Merge patterns from multiple categories.
+
+        Args:
+            patterns_by_category: Dict mapping category names to pattern lists.
+            custom_patterns: List of custom user patterns.
+            strategy: Merge strategy - "priority", "append", or "prepend".
+
+        Returns:
+            Tuple of (merged_patterns, conflicts).
+        """
+        if custom_patterns:
+            patterns_by_category["custom"] = custom_patterns
+
+        self._get_category_order(set(patterns_by_category.keys()))
+
+        if strategy == "append":
+            return self._merge_append(patterns_by_category), []
+        elif strategy == "prepend":
+            return self._merge_prepend(patterns_by_category), []
+        else:
+            return self._merge_priority(patterns_by_category)
+
+    def _get_category_order(self, categories: Set[str]) -> List[str]:
+        """Get ordered list of categories based on priority.
+
+        Args:
+            categories: Set of category names.
+
+        Returns:
+            Ordered list of categories.
+        """
+        priority_order = ["os", "ide", "language", "framework", "custom"]
+        ordered = []
+        for cat in priority_order:
+            if cat in categories:
+                ordered.append(cat)
+        for cat in sorted(categories):
+            if cat not in ordered:
+                ordered.append(cat)
+        return ordered
+
+    def _merge_priority(self, patterns_by_category: Dict[str, List[str]]) -> Tuple[List[str], List[str]]:
+        """Merge patterns by priority (lower priority categories first).
+
+        Args:
+            patterns_by_category: Dict mapping category names to pattern lists.
+
+        Returns:
+            Tuple of (merged_patterns, conflicts).
+        """
+        category_order = self._get_category_order(set(patterns_by_category.keys()))
+        seen_patterns: Dict[str, str] = {}
+        merged: List[str] = []
+        conflicts: List[str] = []
+
+        category_patterns: List[Tuple[str, List[str], int]] = []
+        for category in category_order:
+            patterns = patterns_by_category.get(category, [])
+            weight = self.priority_weights.get(category, 0)
+            category_patterns.append((category, patterns, weight))
+
+        category_patterns.sort(key=lambda x: x[2])
+
+        for category, patterns, _ in category_patterns:
+            for pattern in patterns:
+                if not pattern or pattern.strip().startswith("#"):
+                    continue
+
+                normalized = self._normalize_pattern(pattern)
+                if not normalized:
+                    continue
+
+                if normalized in seen_patterns:
+                    if seen_patterns[normalized] != category:
+                        conflicts.append(f"{normalized} (from {seen_patterns[normalized]} and {category})")
+                else:
+                    seen_patterns[normalized] = category
+                    merged.append(pattern)
+
+        return merged, conflicts
+
+    def _merge_append(self, patterns_by_category: Dict[str, List[str]]) -> List[str]:
+        """Merge patterns by appending in order.
+
+        Args:
+            patterns_by_category: Dict mapping category names to pattern lists.
+
+        Returns:
+            List of merged patterns.
+        """
+        category_order = self._get_category_order(set(patterns_by_category.keys()))
+        seen_patterns: Set[str] = set()
+        merged: List[str] = []
+
+        for category in category_order:
+            patterns = patterns_by_category.get(category, [])
+            for pattern in patterns:
+                if not pattern or pattern.strip().startswith("#"):
+                    continue
+                normalized = self._normalize_pattern(pattern)
+                if normalized and normalized not in seen_patterns:
+                    seen_patterns.add(normalized)
+                    merged.append(pattern)
+
+        return merged
+
+    def _merge_prepend(self, patterns_by_category: Dict[str, List[str]]) -> List[str]:
+        """Merge patterns by prepending in order.
+
+        Args:
+            patterns_by_category: Dict mapping category names to pattern lists.
+
+        Returns:
+            List of merged patterns.
+        """
+        category_order = self._get_category_order(set(patterns_by_category.keys()))
+        seen_patterns: Set[str] = set()
+        merged: List[str] = []
+
+        for category in reversed(category_order):
+            patterns = patterns_by_category.get(category, [])
+            section: List[str] = []
+            for pattern in patterns:
+                if not pattern or pattern.strip().startswith("#"):
+                    continue
+                normalized = self._normalize_pattern(pattern)
+                if normalized and normalized not in seen_patterns:
+                    seen_patterns.add(normalized)
+                    section.append(pattern)
+            merged = section + merged
+
+        return merged
+
+    def _normalize_pattern(self, pattern: str) -> Optional[str]:
+        """Normalize a pattern for comparison.
+
+        Args:
+            pattern: Pattern to normalize.
+
+        Returns:
+            Normalized pattern or None.
+        """
+        if not pattern:
+            return None
+
+        pattern = pattern.strip()
+        if not pattern:
+            return None
+
+        if pattern.startswith("#"):
+            return None
+
+        return pattern
+
+    def deduplicate(self, patterns: List[str]) -> List[str]:
+        """Remove duplicate patterns while preserving order.
+
+        Args:
+            patterns: List of patterns to deduplicate.
+
+        Returns:
+            Deduplicated list of patterns.
+        """
+        seen: Set[str] = set()
+        unique: List[str] = []
+
+        for pattern in patterns:
+            normalized = self._normalize_pattern(pattern)
+            if normalized and normalized not in seen:
+                seen.add(normalized)
+                unique.append(pattern)
+
+        return unique
+
+    def resolve_conflict(self, pattern: str, existing: str, resolution: str) -> str:
+        """Resolve a pattern conflict.
+
+        Args:
+            pattern: New pattern being added.
+            existing: Existing pattern.
+            resolution: Resolution strategy - "keep_existing", "keep_new", "combine".
+
+        Returns:
+            Resolved pattern.
+        """
+        if resolution == "keep_existing":
+            return existing
+        elif resolution == "keep_new":
+            return pattern
+        elif resolution == "combine":
+            return f"{existing}\n{pattern}"
+        else:
+            return existing
+
+    def get_pattern_sources(self, patterns: List[str]) -> Dict[str, Set[str]]:
+        """Identify which source files/patterns came from.
+
+        Args:
+            patterns: List of patterns.
+
+        Returns:
+            Dict mapping pattern categories to their patterns.
+        """
+        sources: Dict[str, Set[str]] = {}
+
+        for pattern in patterns:
+            if not pattern or pattern.strip().startswith("#"):
+                continue
+            normalized = self._normalize_pattern(pattern)
+            if normalized:
+                category = self._categorize_pattern(normalized)
+                if category not in sources:
+                    sources[category] = set()
+                sources[category].add(normalized)
+
+        return sources
+
+    def _categorize_pattern(self, pattern: str) -> str:
+        """Categorize a pattern based on its content.
+
+        Args:
+            pattern: Pattern to categorize.
+
+        Returns:
+            Category name.
+        """
+        os_indicators = [".DS_Store", "Thumbs.db", "~"]
+        ide_indicators = [".vscode", ".idea", ".project", ".settings"]
+
+        for indicator in os_indicators:
+            if indicator in pattern:
+                return "os"
+
+        for indicator in ide_indicators:
+            if indicator in pattern:
+                return "ide"
+
+        if "node_modules" in pattern or "*.log" in pattern:
+            return "language"
+
+        return "other"