refactor: extract and modularize core system components

[yordyi]

Summary

This PR refactors the codebase by extracting and modularizing core system components to improve maintainability and code organization.

Key Changes

• RipgrepInstaller: Extracted ripgrep installation logic from ripgrep.ts
• TreeBuilder: Separated file tree construction logic into dedicated module
• TimeoutManager: Added adaptive timeout handling with configurable strategies
• DiagnosticsManager: Centralized LSP diagnostics coordination and event handling
• StreamHandler: Implemented atomic file operations for better data integrity
• MigrationManager: Created extensible database schema migration system
• ReplaceStrategy & Replacers: Modularized text replacement system with multiple strategies

Benefits

• Improved separation of concerns
• Better code reusability
• Enhanced maintainability
• Cleaner architecture
• More testable components

Files Changed

• Modified core files: ripgrep.ts, client.ts, storage.ts, edit.ts, trace/index.ts
• Added 12+ new modular components
• Maintained backward compatibility

Test Plan

• Existing functionality remains unchanged
• All extracted modules maintain the same public APIs
• Enhanced error handling and timeout management

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