docs(readme): sync MCP tool list and config with 1.12.0

- List all 16 shipped tools, grouped by free-core / hosted-intelligence
  /account (was a flat list of 12, missing index_codebase, index_file,
  search_codebase, update_project_soul)
- Replace stale `bun .../src/local/mcp-server.ts` snippets with the
  published `npx -y @virsanghavi/axis-server` wrapper
- Point teams at the hosted /api/mcp backend

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>