Remove MCP code and associated functions

[Nayshins]

This was getting ahead of itself, and now going to wait for an officially supported rust mcp crate

[mentatbot]

I'm getting to work. See my steps and track my cost here.

• Wake on any new activity.
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[mentatbot]

PR Review - Removal of MCP Code

I've reviewed the PR which removes the Model Context Protocol (MCP) code and associated functions from the codebase. This appears to be a clean and thorough removal of a feature that was added prematurely, as noted in the PR description.

Changes Assessment

• ✅ Complete removal of all MCP-related functionality
• ✅ Removed the Serve CLI command
• ✅ Deleted all MCP-specific modules and files
• ✅ Removed MCP-related functionality from the knowledge graph implementation
• ✅ Updated tests to match the new (reduced) functionality

Observations

• Some of the removed functionality in knowledge_graph.rs could potentially be useful independent of MCP (like search capabilities and relationship exploration). If these are needed later, they can be re-added in a more focused way.
• There are some whitespace-only changes in files like benches/parsing_benchmarks.rs, but these appear to be harmless formatting adjustments.

The changes look good to me. Waiting for CI to complete, but the changes are well-structured and focused on the single concern of removing MCP code.