refactor(mcp): replace deprecated ToolboxAPI calls with toolbox-api-client

[MDzaja]

Summary by cubic

Replaced deprecated ToolboxAPI calls with toolbox-api-client in the MCP toolbox proxy. Removed Toolbox endpoints/models from the Go/Java API clients and OpenAPI, and updated sdk-ruby to use DaytonaToolboxApiClient models for replace_in_files and LSP completions.

• Refactors

  • Dropped ToolboxAPI from api-client-go and api-client-java, removed Toolbox-related models, and pruned api/openapi.yaml. Other APIs are unchanged.
  • Ruby SDK: pointed replace_in_files and LSP completions at DaytonaToolboxApiClient models.

• Migration

  • Go: APIClient.ToolboxAPI no longer exists. Replace calls with toolbox-api-client equivalents and update imports.
  • Java: Remove io.daytona.api.client.api.ToolboxApi and related models. Use the toolbox-api-client instead and update imports/serializers as needed.
  • Ruby: If using Toolbox models directly, import from DaytonaToolboxApiClient. No other changes needed.
  • No behavior changes outside Toolbox-related code paths.

^{Written for commit 9b539e2. Summary will update on new commits.}

[cubic-dev-ai]

All reported issues were addressed across 505 files

Not reviewed (too large): openapi-specs/api.json (~14,348 lines) - if these are generated or fixture files, add them to ignored paths to exclude them from future reviews.

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<sub>Note: This PR contains a large number of files. cubic only reviews up to 200 files per PR, so some files may not have been reviewed. cubic prioritizes the most important files to review.
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