refactor: extract clustering system to cluster package

- Create cluster/merkle.go with Merkle tree operations
- Create cluster/gossip.go with gossip protocol implementation
- Create cluster/sync.go with data synchronization logic
- Create cluster/bootstrap.go with cluster joining functionality

Major clustering functionality now properly separated:
* MerkleService: Tree building, hashing, filtering
* GossipService: Member discovery, health checking, list merging
* SyncService: Merkle-based synchronization between nodes
* BootstrapService: Seed node joining and initial sync

Build tested and verified working. Ready for main.go integration.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

cluster/merkle.go

@@ -0,0 +1,176 @@
+package cluster
+
+import (
+	"bytes"
+	"crypto/sha256"
+	"encoding/json"
+	"fmt"
+	"sort"
+	"strconv"
+	"strings"
+
+	badger "github.com/dgraph-io/badger/v4"
+	"github.com/sirupsen/logrus"
+
+	"kvs/types"
+)
+
+// MerkleService handles Merkle tree operations
+type MerkleService struct {
+	db     *badger.DB
+	logger *logrus.Logger
+}
+
+// NewMerkleService creates a new Merkle tree service
+func NewMerkleService(db *badger.DB, logger *logrus.Logger) *MerkleService {
+	return &MerkleService{
+		db:     db,
+		logger: logger,
+	}
+}
+
+// CalculateHash generates a SHA256 hash for a given byte slice
+func CalculateHash(data []byte) []byte {
+	h := sha256.New()
+	h.Write(data)
+	return h.Sum(nil)
+}
+
+// CalculateLeafHash generates a hash for a leaf node based on its path, UUID, timestamp, and data
+func (s *MerkleService) CalculateLeafHash(path string, storedValue *types.StoredValue) []byte {
+	// Concatenate path, UUID, timestamp, and the raw data bytes for hashing
+	// Ensure a consistent order of fields for hashing
+	dataToHash := bytes.Buffer{}
+	dataToHash.WriteString(path)
+	dataToHash.WriteByte(':')
+	dataToHash.WriteString(storedValue.UUID)
+	dataToHash.WriteByte(':')
+	dataToHash.WriteString(strconv.FormatInt(storedValue.Timestamp, 10))
+	dataToHash.WriteByte(':')
+	dataToHash.Write(storedValue.Data) // Use raw bytes of json.RawMessage
+
+	return CalculateHash(dataToHash.Bytes())
+}
+
+// GetAllKVPairsForMerkleTree retrieves all key-value pairs needed for Merkle tree construction
+func (s *MerkleService) GetAllKVPairsForMerkleTree() (map[string]*types.StoredValue, error) {
+	pairs := make(map[string]*types.StoredValue)
+	err := s.db.View(func(txn *badger.Txn) error {
+		opts := badger.DefaultIteratorOptions
+		opts.PrefetchValues = true // We need the values for hashing
+		it := txn.NewIterator(opts)
+		defer it.Close()
+
+		// Iterate over all actual data keys (not _ts: indexes)
+		for it.Rewind(); it.Valid(); it.Next() {
+			item := it.Item()
+			key := string(item.Key())
+
+			if strings.HasPrefix(key, "_ts:") {
+				continue // Skip index keys
+			}
+
+			var storedValue types.StoredValue
+			err := item.Value(func(val []byte) error {
+				return json.Unmarshal(val, &storedValue)
+			})
+			if err != nil {
+				s.logger.WithError(err).WithField("key", key).Warn("Failed to unmarshal stored value for Merkle tree, skipping")
+				continue
+			}
+			pairs[key] = &storedValue
+		}
+		return nil
+	})
+	if err != nil {
+		return nil, err
+	}
+	return pairs, nil
+}
+
+// BuildMerkleTreeFromPairs constructs a Merkle Tree from the KVS data
+// This version uses a recursive approach to build a balanced tree from sorted keys
+func (s *MerkleService) BuildMerkleTreeFromPairs(pairs map[string]*types.StoredValue) (*types.MerkleNode, error) {
+	if len(pairs) == 0 {
+		return &types.MerkleNode{Hash: CalculateHash([]byte("empty_tree")), StartKey: "", EndKey: ""}, nil
+	}
+
+	// Sort keys to ensure consistent tree structure
+	keys := make([]string, 0, len(pairs))
+	for k := range pairs {
+		keys = append(keys, k)
+	}
+	sort.Strings(keys)
+
+	// Create leaf nodes
+	leafNodes := make([]*types.MerkleNode, len(keys))
+	for i, key := range keys {
+		storedValue := pairs[key]
+		hash := s.CalculateLeafHash(key, storedValue)
+		leafNodes[i] = &types.MerkleNode{Hash: hash, StartKey: key, EndKey: key}
+	}
+
+	// Recursively build parent nodes
+	return s.buildMerkleTreeRecursive(leafNodes)
+}
+
+// buildMerkleTreeRecursive builds the tree from a slice of nodes
+func (s *MerkleService) buildMerkleTreeRecursive(nodes []*types.MerkleNode) (*types.MerkleNode, error) {
+	if len(nodes) == 0 {
+		return nil, nil
+	}
+	if len(nodes) == 1 {
+		return nodes[0], nil
+	}
+
+	var nextLevel []*types.MerkleNode
+	for i := 0; i < len(nodes); i += 2 {
+		left := nodes[i]
+		var right *types.MerkleNode
+		if i+1 < len(nodes) {
+			right = nodes[i+1]
+		}
+
+		var combinedHash []byte
+		var endKey string
+
+		if right != nil {
+			combinedHash = CalculateHash(append(left.Hash, right.Hash...))
+			endKey = right.EndKey
+		} else {
+			// Odd number of nodes, promote the left node
+			combinedHash = left.Hash
+			endKey = left.EndKey
+		}
+
+		parentNode := &types.MerkleNode{
+			Hash:     combinedHash,
+			StartKey: left.StartKey,
+			EndKey:   endKey,
+		}
+		nextLevel = append(nextLevel, parentNode)
+	}
+	return s.buildMerkleTreeRecursive(nextLevel)
+}
+
+// FilterPairsByRange filters a map of StoredValue by key range
+func FilterPairsByRange(allPairs map[string]*types.StoredValue, startKey, endKey string) map[string]*types.StoredValue {
+	filtered := make(map[string]*types.StoredValue)
+	for key, value := range allPairs {
+		if (startKey == "" || key >= startKey) && (endKey == "" || key <= endKey) {
+			filtered[key] = value
+		}
+	}
+	return filtered
+}
+
+// BuildSubtreeForRange builds a Merkle subtree for a specific key range
+func (s *MerkleService) BuildSubtreeForRange(startKey, endKey string) (*types.MerkleNode, error) {
+	pairs, err := s.GetAllKVPairsForMerkleTree()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get KV pairs for subtree: %v", err)
+	}
+	
+	filteredPairs := FilterPairsByRange(pairs, startKey, endKey)
+	return s.BuildMerkleTreeFromPairs(filteredPairs)
+}