feat: Implement foundation layer with domain entities and repository interfaces

- Add complete domain layer: Note, Vault, WikiLink, Tag, Frontmatter, Graph entities
- Implement repository interfaces for data access abstraction
- Create comprehensive configuration system with YAML and env support
- Add CLI entry point with signal handling and graceful shutdown
- Fix mermaid diagram syntax in design.md (array notation)
- Add CLAUDE.md for development guidance

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

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

internal/domain/graph.go

@@ -0,0 +1,117 @@
+package domain
+
+import "sync"
+
+type Graph struct {
+	adjacencyList map[string]map[string]bool
+	mutex         sync.RWMutex
+}
+
+func NewGraph() *Graph {
+	return &Graph{
+		adjacencyList: make(map[string]map[string]bool),
+	}
+}
+
+func (g *Graph) AddEdge(from, to string) {
+	g.mutex.Lock()
+	defer g.mutex.Unlock()
+
+	if g.adjacencyList[from] == nil {
+		g.adjacencyList[from] = make(map[string]bool)
+	}
+	g.adjacencyList[from][to] = true
+}
+
+func (g *Graph) RemoveEdge(from, to string) {
+	g.mutex.Lock()
+	defer g.mutex.Unlock()
+
+	if g.adjacencyList[from] != nil {
+		delete(g.adjacencyList[from], to)
+		if len(g.adjacencyList[from]) == 0 {
+			delete(g.adjacencyList, from)
+		}
+	}
+}
+
+func (g *Graph) GetOutlinks(path string) []string {
+	g.mutex.RLock()
+	defer g.mutex.RUnlock()
+
+	var outlinks []string
+	if targets, exists := g.adjacencyList[path]; exists {
+		for target := range targets {
+			outlinks = append(outlinks, target)
+		}
+	}
+	return outlinks
+}
+
+func (g *Graph) GetBacklinks(path string) []string {
+	g.mutex.RLock()
+	defer g.mutex.RUnlock()
+
+	var backlinks []string
+	for source, targets := range g.adjacencyList {
+		if targets[path] {
+			backlinks = append(backlinks, source)
+		}
+	}
+	return backlinks
+}
+
+func (g *Graph) HasEdge(from, to string) bool {
+	g.mutex.RLock()
+	defer g.mutex.RUnlock()
+
+	if targets, exists := g.adjacencyList[from]; exists {
+		return targets[to]
+	}
+	return false
+}
+
+func (g *Graph) RemoveNode(path string) {
+	g.mutex.Lock()
+	defer g.mutex.Unlock()
+
+	delete(g.adjacencyList, path)
+
+	for source, targets := range g.adjacencyList {
+		delete(targets, path)
+		if len(targets) == 0 {
+			delete(g.adjacencyList, source)
+		}
+	}
+}
+
+func (g *Graph) GetAllNodes() []string {
+	g.mutex.RLock()
+	defer g.mutex.RUnlock()
+
+	nodeSet := make(map[string]bool)
+
+	for source := range g.adjacencyList {
+		nodeSet[source] = true
+	}
+
+	for _, targets := range g.adjacencyList {
+		for target := range targets {
+			nodeSet[target] = true
+		}
+	}
+
+	var nodes []string
+	for node := range nodeSet {
+		nodes = append(nodes, node)
+	}
+
+	return nodes
+}
+
+func (g *Graph) Clear() {
+	g.mutex.Lock()
+	defer g.mutex.Unlock()
+
+	g.adjacencyList = make(map[string]map[string]bool)
+}