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>

CLAUDE.md

@@ -0,0 +1,134 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Development Commands
+
+### Building
+```bash
+go build -o obsidian-mcp ./cmd/obsidian-mcp
+```
+
+### Testing
+```bash
+# Run all tests
+go test ./...
+
+# Run tests with coverage
+go test -cover ./...
+
+# Run tests for specific package
+go test ./internal/domain/
+
+# Run specific test
+go test -run TestNoteName ./internal/domain/
+```
+
+### Running
+```bash
+# Basic run with vault path
+./obsidian-mcp --vault /path/to/vault
+
+# With config file
+./obsidian-mcp --config config.yaml
+
+# With environment variables
+VAULT_PATH=/path/to/vault LOG_LEVEL=debug ./obsidian-mcp
+```
+
+### Dependencies
+```bash
+# Download dependencies
+go mod download
+
+# Update dependencies
+go mod tidy
+
+# Add new dependency
+go get github.com/package/name
+```
+
+## Architecture Overview
+
+This is an Obsidian MCP (Model Context Protocol) Server implementing **Clean Architecture** with strict dependency inversion. The codebase follows Domain-Driven Design principles.
+
+### Layer Dependencies (Dependency Rule)
+All dependencies point inward toward the domain:
+- **Domain Layer** (innermost): Pure business logic, no external dependencies
+- **Repository Layer**: Interfaces defining data access contracts
+- **Use Case Layer**: Business orchestration, depends only on domain + repository interfaces
+- **Infrastructure Layer**: Concrete implementations (filesystem, git, parsers)
+- **Adapter Layer**: MCP protocol handlers, DTOs, external interface adapters
+
+### Key Domain Entities
+
+**Note**: Central entity representing an Obsidian note with:
+- Path validation (must end in .md, no path traversal)
+- Content with automatic extraction of WikiLinks and Tags
+- Frontmatter (YAML metadata)
+- Timestamps (created/modified)
+
+**Vault**: Aggregate root managing collections of notes with:
+- Graph of note relationships
+- Tag indexing with counts
+- Statistics calculation
+
+**WikiLink**: Value object for `[[Internal Links]]` with support for:
+- Aliases: `[[target|display text]]`
+- Sections: `[[note#section]]`
+
+**Tag**: Value object for `#tags` with:
+- Nested tag support: `#project/ai/research`
+- Validation (no spaces, proper format)
+
+**Graph**: Thread-safe adjacency list for note relationships
+
+### Repository Pattern
+All data access goes through interfaces in `internal/repository/`:
+- **NoteRepository**: CRUD operations for notes
+- **GitRepository**: Version control operations
+- **VaultRepository**: Vault-level operations and statistics
+- **SearchIndex**: Full-text search capabilities
+- **GraphIndex**: Backlink/outlink indexing
+- **TagIndex**: Tag-based search and operations
+
+### Configuration System
+Uses `internal/config/config.go` with:
+- YAML file configuration
+- Environment variable overrides
+- Validation with sensible defaults
+- Support for vault path, git settings, caching, logging, performance tuning
+
+### Error Handling
+Domain errors defined in `internal/domain/errors.go`:
+- `ErrNoteNotFound`, `ErrNoteAlreadyExists`
+- `ErrInvalidPath`, `ErrInvalidTag`
+- `ErrCircularLink`
+
+### Key Architectural Patterns
+
+1. **Dependency Inversion**: Use cases depend on repository interfaces, not implementations
+2. **Entity Encapsulation**: Domain entities manage their own business rules
+3. **Value Objects**: Immutable types like WikiLink, Tag, Frontmatter
+4. **Repository Pattern**: Clean separation between business logic and data access
+5. **Configuration as Code**: Comprehensive config system with validation
+
+### Implementation Status
+Currently implemented:
+- ✅ Complete domain layer with all entities
+- ✅ All repository interfaces
+- ✅ Configuration system
+- ✅ CLI entry point
+
+Still needed (per design.md roadmap):
+- Infrastructure implementations (filesystem, git, markdown parsing)
+- Use case implementations
+- MCP adapter layer with 45+ tools
+- Index implementations (search, graph, tag)
+
+### MCP Integration
+When implementing MCP tools, they should:
+- Live in `internal/adapter/mcp/tools/`
+- Use DTOs from `internal/adapter/dto/`
+- Call use cases, never repositories directly
+- Handle MCP protocol specifics while keeping business logic in use cases