feat: implement apply_code tool for two-stage code generation (#6159)

[roomote]

This PR implements the apply_code tool as proposed in issue #6159, providing a more reliable alternative to apply_diff for code modifications.

Summary

The apply_code tool uses a two-stage approach to improve code modification reliability:

1. Stage 1: Creative code generation based on instructions (without diff context noise)
2. Stage 2: Focused diff generation with clean context

Changes

• Added new applyCodeTool.ts that implements the two-stage workflow
• Added applyEnabled configuration option to enable/disable the feature (opt-in)
• Updated tool type definitions and registries across the codebase
• Created tool description document for the system prompt
• Added comprehensive unit tests for the new functionality
• Integrated with existing diff application infrastructure

Key Benefits

• Separates creative code generation from technical diff creation
• Reduces errors caused by noisy conversational contexts
• Uses structured JSON output for reliable parsing
• Maintains backward compatibility (opt-in feature)
• Leverages existing diff tools for actual file modifications

Testing

• Added comprehensive test suite covering all edge cases
• Verified existing tests still pass (no regressions)
• Tests cover parameter validation, feature flags, file operations, and error handling

Closes #6159

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Important

Introduces apply_code tool for two-stage code generation and diff application, with configuration, integration, and comprehensive testing.

• Behavior:
  • Implements apply_code tool in applyCodeTool.ts for two-stage code generation and diff application.
  • Adds applyEnabled config option in provider-settings.ts to enable/disable the tool.
  • Integrates apply_code with existing infrastructure in presentAssistantMessage.ts.
• Tool Descriptions:
  • Adds getApplyCodeDescription() in apply-code.ts.
  • Updates tool.ts and index.ts to include apply_code in tool registries.
• Testing:
  • Adds applyCodeTool.spec.ts with comprehensive tests for parameter validation, feature flags, file operations, and error handling.
• Misc:
  • Updates ExtensionMessage.ts and tools.ts to support new tool parameters and types.

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[daniel-lxs]

This is basically generating a unified diff, models are not good at generating or applying unified diff, if anything this should rewrite an updated file.