knowledge_graph_builder

Imported from Phoenix-Chen-Git/knowledge_graph_builder (AGENTS.md). Install upstream with npx skills add Phoenix-Chen-Git/knowledge_graph_builder. Copyright stays with the author.

AGENTS.md

This file provides guidance to any coding agent when working with code in this repository.

Overview

Copilot for Obsidian is an AI-powered assistant plugin that integrates various LLM providers (OpenAI, Anthropic, Google, etc.) with Obsidian. It provides chat interfaces, autocomplete, semantic search, and various AI-powered commands for note-taking and knowledge management.

Development Commands

Build & Development

• NEVER RUN npm run dev - The user will handle all builds manually
• npm run build - Production build (TypeScript check + minified output)

Code Quality

• npm run lint - Run ESLint checks
• npm run lint:fix - Auto-fix ESLint issues
• npm run format - Format code with Prettier
• npm run format:check - Check formatting without changing files
• Before PR: Always run npm run format && npm run lint

Testing

• npm run test - Run unit tests (excludes integration tests)
• npm run test:integration - Run integration tests (requires API keys)
• Run single test: npm test -- -t "test name"

High-Level Architecture

Core Systems

1. LLM Provider System (src/LLMProviders/)

   • Provider implementations for OpenAI, Anthropic, Google, Azure, local models
   • LLMProviderManager handles provider lifecycle and switching
   • Stream-based responses with error handling and rate limiting
   • Custom model configuration support

2. Chain Factory Pattern (src/chainFactory.ts)

   • Different chain types for various AI operations (chat, copilot, adhoc prompts)
   • LangChain integration for complex workflows
   • Memory management for conversation context
   • Tool integration (search, file operations, time queries)

3. Vector Store & Search (src/search/)

   • VectorStoreManager manages embeddings and semantic search
   • ChunkedStorage for efficient large document handling
   • Event-driven index updates via IndexManager
   • Multiple embedding providers support

4. UI Component System (src/components/)

   • React functional components with Radix UI primitives
   • Tailwind CSS with class variance authority (CVA)
   • Modal system for user interactions
   • Chat interface with streaming support
   • Settings UI with versioned components

5. Message Management Architecture (src/core/, src/state/)

   • MessageRepository (src/core/MessageRepository.ts): Single source of truth for all messages
     • Stores each message once with both displayText and processedText
     • Provides computed views for UI display and LLM processing
     • No complex dual-array synchronization
   • ChatManager (src/core/ChatManager.ts): Central business logic coordinator
     • Orchestrates MessageRepository, ContextManager, and LLM operations
     • Handles message sending, editing, regeneration, and deletion
     • Manages context processing and chain memory synchronization
     • Project Chat Isolation: Maintains separate MessageRepository per project
       • Automatically detects project switches via getCurrentMessageRepo()
       • Each project has its own isolated message history
       • Non-project chats use defaultProjectKey repository
   • ChatUIState (src/state/ChatUIState.ts): Clean UI-only state manager
     • Delegates all business logic to ChatManager
     • Provides React integration with subscription mechanism
     • Replaces legacy SharedState with minimal, focused approach
   • ContextManager (src/core/ContextManager.ts): Handles context processing
     • Processes message context (notes, URLs, selected text)
     • Reprocesses context when messages are edited

6. Settings Management

   • Jotai for atomic settings state management
   • React contexts for feature-specific state

7. Plugin Integration

   • Main entry: src/main.ts extends Obsidian Plugin
   • Command registration system
   • Event handling for Obsidian lifecycle
   • Settings persistence and migration
   • Chat history loading via pending message mechanism

Key Patterns

• Single Source of Truth: MessageRepository stores each message once with computed views
• Clean Architecture: Repository → Manager → UIState → React Components
• Context Reprocessing: Automatic context updates when messages are edited
• Computed Views: Display messages for UI, LLM messages for AI processing
• Project Isolation: Each project maintains its own MessageRepository instance
• Error Handling: Custom error types with detailed interfaces
• Async Operations: Consistent async/await pattern with proper error boundaries
• Caching: Multi-layer caching for files, PDFs, and API responses
• Streaming: Real-time streaming for LLM responses
• Testing: Unit tests adjacent to implementation, integration tests for API calls

Message Management Architecture

For detailed architecture diagrams and documentation, see MESSAGE_ARCHITECTURE.md.

Core Classes and Flow

1. MessageRepository (src/core/MessageRepository.ts)

   • Single source of truth for all messages
   • Stores StoredMessage objects with both displayText and processedText
   • Provides computed views via getDisplayMessages() and getLLMMessages()
   • No complex dual-array synchronization or ID matching

2. ChatManager (src/core/ChatManager.ts)

   • Central business logic coordinator
   • Orchestrates MessageRepository, ContextManager, and LLM operations
   • Handles all message CRUD operations with proper error handling
   • Synchronizes with chain memory for conversation history
   • Project Chat Isolation Implementation:
     • Maintains projectMessageRepos: Map<string, MessageRepository> for project-specific storage
     • getCurrentMessageRepo() automatically detects current project and returns correct repository
     • Seamlessly switches between project repositories when project changes
     • Creates new empty repository for each project (no message caching)

3. ChatUIState (src/state/ChatUIState.ts)

   • Clean UI-only state manager
   • Delegates all business logic to ChatManager
   • Provides React integration with subscription mechanism
   • Replaces legacy SharedState with minimal, focused approach

4. ContextManager (src/core/ContextManager.ts)

   • Handles context processing (notes, URLs, selected text)
   • Reprocesses context when messages are edited
   • Ensures fresh context for LLM processing

5. ChatPersistenceManager (src/core/ChatPersistenceManager.ts)

   • Handles saving and loading chat history to/from markdown files
   • Project-aware file naming (prefixes with project ID)
   • Parses and formats chat content for storage
   • Integrated with ChatManager for seamless persistence

Code Style Guidelines

MAJOR PRINCIPLES

• ALWAYS WRITE GENERALIZABLE SOLUTIONS: Never add edge-case handling or hardcoded logic for specific scenarios (like "piano notes" or "daily notes"). Solutions must work for all cases.
• NEVER MODIFY AI PROMPT CONTENT: Do not update, edit, or change any AI prompts, system prompts, or model adapter prompts unless explicitly asked to do so by the user
• Avoid hardcoding: No hardcoded folder names, file patterns, or special-case logic
• Configuration over convention: If behavior needs to vary, make it configurable, not hardcoded
• Universal patterns: Solutions should work equally well for any folder structure, naming convention, or content type

TypeScript

• Strict mode enabled (no implicit any, strict null checks)
• Use absolute imports with @/ prefix: import { ChainType } from "@/chainFactory"
• Prefer const assertions and type inference where appropriate
• Use interface for object shapes, type for unions/aliases

React

• Functional components only (no class components)
• Custom hooks for reusable logic
• Props interfaces defined above components
• Avoid inline styles, use Tailwind classes

General

• File naming: PascalCase for components, camelCase for utilities
• Async/await over promises
• Early returns for error conditions
• Always add JSDoc comments for all functions and methods
• Organize imports: React → external → internal
• Avoid language-specific lists (like stopwords or action verbs) - use language-agnostic approaches instead

Logging

• NEVER use console.log - Use the logging utilities instead:
  • logInfo() for informational messages
  • logWarn() for warnings
  • logError() for errors
• Import from logger: import { logInfo, logWarn, logError } from "@/logger"

Testing Guidelines

• Unit tests use Jest with TypeScript support
• Mock Obsidian API for plugin testing
• Integration tests require API keys in .env.test
• Test files adjacent to implementation (.test.ts)
• Use @testing-library/react for component testing

Development Session Planning

Using TODO.md for Session Management

IMPORTANT: When working on a development session, maintain a comprehensive TODO.md file that serves as the central plan and tracker:

1. Session Goal: Define the high-level objective at the start
2. Task Tracking:
   • List all completed tasks with [x] checkboxes
   • Track pending tasks with [ ] checkboxes
   • Group related tasks into logical sections
3. Architecture Decisions: Document key design choices and rationale
4. Progress Updates: Keep the TODO.md updated as tasks complete
5. Testing Checklist: Include verification steps for the session

The TODO.md should be:

• The single source of truth for session progress
• Updated frequently as work progresses
• Clear enough that another developer can understand what was done
• Comprehensive enough to serve as a migration guide

Structure Example:

# Development Session TODO

## Session Goal

[Clear statement of what this session aims to achieve]

## Completed Tasks ✅

- [x] Task description with key details
- [x] Another completed task

## Pending Tasks 📋

- [ ] Next task to work on
- [ ] Future enhancement

## Architecture Summary

[Key design decisions and rationale]

## Testing Checklist

- [ ] Functionality verification
- [ ] Performance checks

Important Notes

• The plugin supports multiple LLM providers with custom endpoints
• Vector store requires rebuilding when switching embedding providers
• Settings are versioned - migrations may be needed
• Local model support available via Ollama/LM Studio
• Rate limiting is implemented for all API calls
• For technical debt and known issues, see TECHDEBT.md
• For current development session planning, see TODO.md

Obsidian Plugin Environment

• Global app variable: In Obsidian plugins, app is a globally available variable that provides access to the Obsidian API. It's automatically available in all files without needing to import or declare it.

Architecture Migration Notes

• SharedState Removed: The legacy src/sharedState.ts has been completely removed
• Clean Architecture: New architecture follows Repository → Manager → UIState → UI pattern
• Single Source of Truth: All messages stored once in MessageRepository with computed views
• Context Always Fresh: Context is reprocessed when messages are edited to ensure accuracy
• Chat History Loading: Uses pending message mechanism through CopilotView → Chat component props
• Project Chat Isolation: Each project now has completely isolated chat history
  • Automatic detection of project switches via ProjectManager.getCurrentProjectId()
  • Separate MessageRepository instances per project ID
  • Non-project chats stored in default repository
  • Backwards compatible - loads existing messages from ProjectManager cache
  • Zero configuration required - works automatically