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/vault_repository.go

@@ -0,0 +1,39 @@
+package repository
+
+import (
+	"context"
+
+	"github.com/user/obsidian-mcp-server/internal/domain"
+)
+
+type VaultStructure struct {
+	Name     string            `json:"name"`
+	Path     string            `json:"path"`
+	Type     string            `json:"type"` // "file" or "directory"
+	Children []*VaultStructure `json:"children,omitempty"`
+}
+
+type MostLinkedNote struct {
+	Path  string `json:"path"`
+	Count int    `json:"count"`
+}
+
+type VaultStats struct {
+	TotalNotes     int               `json:"total_notes"`
+	TotalWords     int               `json:"total_words"`
+	TotalLinks     int               `json:"total_links"`
+	TotalTags      int               `json:"total_tags"`
+	AvgNoteLength  int               `json:"avg_note_length"`
+	MostLinked     []*MostLinkedNote `json:"most_linked"`
+	OrphanedNotes  int               `json:"orphaned_notes"`
+	LastIndexed    string            `json:"last_indexed"`
+}
+
+type VaultRepository interface {
+	GetStats(ctx context.Context) (*VaultStats, error)
+	GetStructure(ctx context.Context, maxDepth int) (*VaultStructure, error)
+	FindOrphaned(ctx context.Context, excludePaths []string) ([]string, error)
+	GetMostLinked(ctx context.Context, limit int) ([]*MostLinkedNote, error)
+	Initialize(ctx context.Context, vault *domain.Vault) error
+	Rebuild(ctx context.Context) error
+}