Major Enhancement: Production-Ready TypeScript Refactor with Testing, CI/CD, and New Features

[ddebowczyk]

Overview

This PR transforms QMD into a production-ready tool with comprehensive testing, modular architecture, CI/CD pipeline, and significant new features. 50 commits containing systematic improvements across all areas of the codebase.

🎯 Major Achievements

1. Complete TypeScript Refactoring (Modular Architecture)

• Migrated to oclif CLI framework for professional command structure
• Extracted modular layers: types, utils, config, database, services, commands
• Repository pattern for database operations with proper separation of concerns
• Eliminated 2000+ line monolith into focused, testable modules
• Full type safety with proper TypeScript interfaces and Zod validation

2. Comprehensive Test Suite (Coverage: ~90%)

• 150+ tests across all layers (unit, integration, E2E)
• Test infrastructure: fixtures, mocks, in-memory databases
• Security tests: SQL injection prevention, input sanitization
• Edge case coverage: error handling, race conditions, concurrent operations
• CI integration: automated testing on push/PR

3. GitHub Actions CI/CD Pipeline

• Multi-platform testing (Ubuntu, macOS, Windows)
• Automated checks: tests, type checking, build verification
• Code coverage reporting with Codecov integration
• Quality gates for pull requests

4. New Commands & Features

qmd init - Project Initialization

• Creates .qmd/ directory for project-local indexes
• Auto-generates .gitignore to exclude SQLite files
• Optional --with-index flag for immediate indexing
• Optional --config flag to generate config file

qmd doctor - Health Diagnostics

• Validates project configuration and dependencies
• Tests Ollama connectivity and models
• Checks database schema integrity and migrations
• Identifies orphaned records and data issues
• Reports statistics and suggests fixes
• Auto-fix capability for common issues

qmd update - Collection Re-indexing

• qmd update - Re-index all collections
• qmd update <id> - Update specific collection
• Incremental updates (no need to delete/re-add)
• Works from any subdirectory

qmd cleanup - Database Maintenance

• Removes soft-deleted documents from database
• Cleans up orphaned vectors and path contexts
• Runs VACUUM for database optimization
• Reports space saved

5. Unified Configuration System

Priority: CLI flags > Environment variables > Config file > Defaults

Config File (.qmd/config.json)

{
  "embedModel": "nomic-embed-text",
  "rerankModel": "qwen3-reranker:0.6b-q8_0",
  "defaultGlob": "**/*.md",
  "excludeDirs": ["node_modules", ".git"],
  "ollamaUrl": "http://localhost:11434"
}

Environment Variables

• QMD_EMBED_MODEL - Override embedding model
• QMD_RERANK_MODEL - Override reranking model
• QMD_CACHE_DIR - Custom cache location
• OLLAMA_URL - Ollama server URL

CLI Flags

• --embed-model - Per-command model override
• --rerank-model - Per-command reranker override

6. Project-Local Index Support

• .qmd/ directory for project-specific indexes (like .git/)
• Auto-detection walks up directory tree
• Works from subdirectories - no need to cd to root
• Shareable config via .qmd/config.json

Index Location Priority:

1. .qmd/ directory (project-local, walks up tree)
2. QMD_CACHE_DIR environment variable
3. ~/.cache/qmd/ (global default)

7. Enhanced Features & Improvements

Search & Indexing

• Search history tracking (stored in SQLite, not files)
• Improved glob pattern handling (prevents shell expansion issues)
• Performance optimizations: batch operations, ANALYZE, proper indexing
• Database migrations with structured migration system

Code Quality

• Zod schema validation for runtime type safety
• Fixed type-database mismatches across all entities
• Added missing indexes for query performance
• SQL injection prevention with parameterized queries

Documentation

• Comprehensive user docs in docs/user/
• Developer architecture guide in docs/dev/ARCHITECTURE.md
• Updated README with correct models and configuration
• Command reference with examples

8. Bug Fixes & Refinements

• Fixed incorrect embedding model (embeddinggemma → nomic-embed-text)
• Removed terminal escape codes when output is not a TTY
• Added --version command for version display
• Fixed type mismatches in Collection, Document, PathContext, OllamaCache
• Improved error messages and user feedback

📊 Statistics

• 50 commits with clear, descriptive messages
• 74 tracked issues completed (via beads workflow)
• 150+ tests across 20+ test files
• ~90% code coverage
• 0 open issues - all work completed
• 0.8 hours average lead time per issue

🏗️ Architecture Improvements

Before: Single 2000+ line qmd.ts file
After: Modular structure

src/
├── commands/       # oclif commands (8 commands)
├── services/       # Business logic (ollama, embedding, search, reranking)
├── database/       # Data access layer (repositories, migrations)
├── models/         # Types and schemas
├── config/         # Configuration and constants
└── utils/          # Shared utilities (hash, paths, terminal)

🧪 Testing Strategy

1. Unit Tests: Individual functions and modules
2. Integration Tests: Database operations, service interactions
3. E2E Tests: Complete workflows (indexing, search, embedding)
4. Security Tests: SQL injection, input validation
5. Performance Tests: Batch operations, concurrent access

🔄 Migration Path

100% backward compatible - existing indexes work without changes.

Users can gradually adopt new features:

1. Continue using existing workflow (no changes needed)
2. Optionally run qmd init for project-local indexes
3. Optionally create .qmd/config.json for team settings
4. Use new commands (doctor, update, cleanup) as needed

📝 Documentation

• ✅ User guides in docs/user/
• ✅ Architecture documentation in docs/dev/
• ✅ Updated README with examples
• ✅ Command reference with all flags
• ✅ Configuration guide
• ✅ Migration examples

🎁 Benefits to Users

1. Reliability: Comprehensive tests prevent regressions
2. Maintainability: Modular code is easier to extend
3. Discoverability: qmd doctor helps troubleshoot issues
4. Flexibility: Unified config system (CLI > env > file > defaults)
5. Team-friendly: Shareable project configs via .qmd/config.json
6. Performance: Optimized queries, batch operations, proper indexes
7. Quality: CI/CD ensures code quality on every change

🔍 Review Notes

This is a large PR but every commit is atomic and well-tested:

• Refactoring was done in phases (Phase 1-8)
• Each phase has corresponding tests
• All tests pass on main branch
• CI/CD validates on multiple platforms

The changes maintain full backward compatibility while adding significant value.

🙏 Acknowledgments

All work tracked via beads workflow for transparent project management.

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Ready to merge - all tests passing, documentation complete, no breaking changes.