feat(server): MCP endpoints API consolidation

[anubhav756]

Overview

This PR serves as the foundational layer that will eventually merge all upcoming PRs for the new test harness and new MCP integration tests for multiple databases.

Before	After

Strategy

While the legacy integration tests continue to run over the legacy /api endpoints, we are introducing the new native MCP JSON-RPC harness in parallel. This allows us to verify both pathways side-by-side without breaking existing CI coverage.

To support this, we utilize the --enable-api flag to control whether the server initializes the legacy API handlers or runs in MCP-only mode. This ensures that the new tests can accurately verify the behavior of the server when running in its final intended configuration.

Changes

• Updates to internal/server/server.go to support dynamic execution and flag-controlled initialization.
• Frontend files updated (loadTools.js and runTool.js) to streamline how tools are loaded and invoked in the UI, aligning it with the upcoming native MCP transition.

Checklist

• Ensure the tests and linter pass
• Manually verified functionality of Toolbox UI

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request represents a significant architectural shift, deprecating and removing all native /api endpoints in favor of a unified /mcp JSON-RPC interface. This change streamlines the server's API surface, enhances maintainability, and ensures a consistent interaction model for clients. To guide users through this transition, legacy API calls now receive a 410 Gone response, clearly indicating the new endpoint. The accompanying frontend updates ensure seamless integration with the new JSON-RPC standard.

Highlights

• Native API Endpoints Removed: The legacy /api endpoints for toolset and tool operations have been completely removed from the server.
• Consolidation on MCP: All API interactions are now consolidated onto the /mcp JSON-RPC endpoint, standardizing the communication protocol.
• Legacy API Redirection: Requests to the old /api/* paths now receive an HTTP 410 Gone status with a message directing users to the /mcp endpoint.
• Frontend Updates: The JavaScript frontend has been updated to exclusively use the new /mcp JSON-RPC format for listing tools, fetching details, and invoking tools.
• Error Handling and Testing Refinements: Error response structures were moved to the MCP module, and new Go types were introduced to facilitate robust testing of MCP interactions.

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[gemini-code-assist]

Code Review

This pull request deprecates and removes the legacy /api native endpoints, transitioning the entire system to use the /mcp JSON-RPC endpoint for tool discovery and invocation. The /api routes now return a 410 Gone status with a message guiding users to the /mcp endpoint. Backend error handling logic previously associated with the /api endpoints has been refactored and moved to mcp.go for reuse. The frontend JavaScript (loadTools.js and runTool.js) has been updated to send JSON-RPC requests to /mcp for listing and invoking tools, and to correctly parse the new MCP response format. Tool details are now fetched once and cached client-side, improving performance by reducing redundant network calls. New Go types for MCP requests and responses have been introduced in tests/mcp_types.go to support testing the new MCP-based interactions. No specific feedback was provided in the review comments.

[Yuan325]

Thank you!

[github-actions]

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