docs: sync MCP tool listings

[Derrick-xn]

Summary

• Add codegraph_explore to the README MCP tools table and Claude permission example.
• Include codegraph_explore in the non-MCP codegraph serve help output.
• Add a consistency test so README tool listings, the permission example, and CLI help stay aligned.

Test plan

• npm test -- __tests__/tool-list-consistency.test.ts
• npm run build
• npm test -- __tests__/mcp-initialize.test.ts __tests__/mcp-roots.test.ts __tests__/watcher.test.ts
• npm test was attempted after build; the relevant tests passed, but the full suite hit a local Node 24 V8 WASM OOM and one watcher timeout during the all-files run.

[Derrick-xn]

I added codegraph_explore to the README Claude permission example so it matches the MCP tools table and CLI help. If you intentionally do not want codegraph_explore auto-allowed because it can return source snippets, I’m happy to drop that line and keep this PR limited to docs/help listing consistency.