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/repository/graph_index.go

@@ -0,0 +1,40 @@
+package repository
+
+import (
+	"context"
+
+	"github.com/user/obsidian-mcp-server/internal/domain"
+)
+
+type GraphNode struct {
+	Path  string `json:"path"`
+	Title string `json:"title"`
+}
+
+type GraphEdge struct {
+	From string `json:"from"`
+	To   string `json:"to"`
+}
+
+type GraphData struct {
+	Nodes []*GraphNode `json:"nodes"`
+	Edges []*GraphEdge `json:"edges"`
+}
+
+type BacklinkInfo struct {
+	From    string `json:"from"`
+	Context string `json:"context"`
+	Line    int    `json:"line"`
+}
+
+type GraphIndex interface {
+	AddNote(ctx context.Context, note *domain.Note) error
+	RemoveNote(ctx context.Context, path string) error
+	GetBacklinks(ctx context.Context, path string) ([]*BacklinkInfo, error)
+	GetOutlinks(ctx context.Context, path string) ([]string, error)
+	GetConnected(ctx context.Context, path string, depth int) (*GraphData, error)
+	FindBrokenLinks(ctx context.Context, notePath string) ([]string, error)
+	UpdateLinks(ctx context.Context, oldPath, newPath string) error
+	Rebuild(ctx context.Context, notes []*domain.Note) error
+	Clear() error
+}