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/git_repository.go

@@ -0,0 +1,33 @@
+package repository
+
+import (
+	"context"
+	"time"
+)
+
+type GitStatus struct {
+	Branch    string
+	Modified  []string
+	Untracked []string
+	Staged    []string
+	Ahead     int
+	Behind    int
+}
+
+type Commit struct {
+	Hash    string
+	Author  string
+	Date    time.Time
+	Message string
+	Files   []string
+}
+
+type GitRepository interface {
+	Status(ctx context.Context) (*GitStatus, error)
+	Pull(ctx context.Context) error
+	Push(ctx context.Context) error
+	Commit(ctx context.Context, message string, files []string) error
+	Log(ctx context.Context, path string, limit int) ([]*Commit, error)
+	IsEnabled() bool
+	Clone(ctx context.Context, url string, path string) error
+}

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
+}

internal/repository/note_repository.go

@@ -0,0 +1,18 @@
+package repository
+
+import (
+	"context"
+
+	"github.com/user/obsidian-mcp-server/internal/domain"
+)
+
+type NoteRepository interface {
+	Get(ctx context.Context, path string) (*domain.Note, error)
+	Create(ctx context.Context, note *domain.Note) error
+	Update(ctx context.Context, note *domain.Note) error
+	Delete(ctx context.Context, path string) error
+	List(ctx context.Context, pattern string, recursive bool) ([]*domain.Note, error)
+	Exists(ctx context.Context, path string) bool
+	FindByTag(ctx context.Context, tag string) ([]*domain.Note, error)
+	FindByContent(ctx context.Context, query string) ([]*domain.Note, error)
+}

internal/repository/search_index.go

@@ -0,0 +1,36 @@
+package repository
+
+import (
+	"context"
+
+	"github.com/user/obsidian-mcp-server/internal/domain"
+)
+
+type SearchResult struct {
+	Path     string `json:"path"`
+	Score    float64 `json:"score"`
+	Matches  []*SearchMatch `json:"matches"`
+}
+
+type SearchMatch struct {
+	Line          int    `json:"line"`
+	Content       string `json:"content"`
+	ContextBefore string `json:"context_before"`
+	ContextAfter  string `json:"context_after"`
+}
+
+type SearchQuery struct {
+	Query         string
+	MaxResults    int
+	CaseSensitive bool
+	UseRegex      bool
+	ContextLines  int
+}
+
+type SearchIndex interface {
+	Index(ctx context.Context, note *domain.Note) error
+	Remove(ctx context.Context, path string) error
+	Search(ctx context.Context, query *SearchQuery) ([]*SearchResult, error)
+	Rebuild(ctx context.Context, notes []*domain.Note) error
+	Clear() error
+}

internal/repository/tag_index.go

@@ -0,0 +1,30 @@
+package repository
+
+import (
+	"context"
+
+	"github.com/user/obsidian-mcp-server/internal/domain"
+)
+
+type TagInfo struct {
+	Name   string `json:"name"`
+	Count  int    `json:"count"`
+	Nested bool   `json:"nested"`
+}
+
+type TagFilter struct {
+	Tags         []string
+	Mode         string // "all" or "any"
+	IncludeNested bool
+}
+
+type TagIndex interface {
+	AddNote(ctx context.Context, note *domain.Note) error
+	RemoveNote(ctx context.Context, path string) error
+	GetAllTags(ctx context.Context) ([]*TagInfo, error)
+	GetNotesWithTag(ctx context.Context, tag string) ([]string, error)
+	GetNotesWithTags(ctx context.Context, filter *TagFilter) ([]string, error)
+	RenameTag(ctx context.Context, oldTag, newTag string) error
+	Rebuild(ctx context.Context, notes []*domain.Note) error
+	Clear() error
+}

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
+}