Atlassian's rebuilt MCP server, now generally available, enforces three things on every call. It uses OAuth 2.1 with PKCE, so the agent only gets the user's existing permissions. It sorts tools into read, write and destructive, so clients can ask for confirmation. And it applies admin-level scopes and audit logging. This article shows how to build the same three controls into your own MCP server with the official Python SDK, following the current MCP specification (2026-07-28). What you'll b...