Add missing QLdoc comments to IR.qll classes, predicates, and newtype branches

Agent-Logs-Url: https://github.com/github/codeql/sessions/12c0f9c8-1b85-4db4-b26f-8dbce818aa5a

Co-authored-by: owen-mc <62447351+owen-mc@users.noreply.github.com>

Author: Copilot