Refactor toolAgent structure

[bhouston]

Description

This PR refactors the toolAgent structure to complete the migration from the deprecated toolAgent.ts file to a modular directory structure.

Changes

• Moved the main toolAgent implementation from index.ts to toolAgentCore.ts
• Updated index.ts to re-export from toolAgentCore.ts and other modules
• Removed the deprecated toolAgent.ts file
• Updated all direct imports to use the new structure
• Updated documentation in README.md
• Fixed duplicate re-export issues in toolAgent/index.ts
• Replaced any type with Record<string, unknown> and unknown[] where appropriate
• Removed re-exports from non-index files
• Standardized import paths to use the index.ts file consistently

Benefits

• Clearer code organization with more meaningful file names
• Reduced technical debt by removing deprecated file
• All imports now use the recommended path
• Improved maintainability with modular design
• Follows best practices for re-exports (only in index.ts files)

Testing

All existing functionality continues to work with the new structure. No behavioral changes were made, only structural refactoring.

Closes #92

[bhouston]

Also fixes #91

[sentry-io]

Suspect Issues

This pull request was deployed and Sentry observed the following issues:

• ‼️ AI_APICallError: Bad Request toolAgent(toolAgentCore.ts) View Issue
• ‼️ AI_RetryError: Failed after 3 attempts. Last error: Cannot connect to API: 4008BEEE01000000:error:0A00010B:SSL routines:ssl3_get_record:wrong version number:../deps/openssl/openssl/ssl/record/ssl3_record.c:355: toolAgent(toolAgentCore.ts) View Issue
• ‼️ AI_APICallError: Invalid JSON response toolAgent(toolAgentCore.ts) View Issue
• ‼️ Error: Error calling Anthropic API: 400 {"type":"error","error":{"type":"invalid_request_error","message":"messages.2: tool_result blocks can only be in user messages"}} AnthropicProvider.generateText(anthropic.ts) View Issue

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[github-actions]

🎉 This PR is included in version mycoder-agent-v1.0.0 🎉

The release is available on:

• npm package (@latest dist-tag)
• GitHub release

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