Query loading/timing state extracted into a standalone store class

The main REPL now tracks query loading and timing (isQueryActive, isExternalLoading, isLoading, submitCount, lastQueryCompletionTime, and the abort controller) in a dedicated class instead of a mix of React state and refs. The class publishes changes to subscribers and mirrors turn start and paused-time into the transcript, and token-count resets now also write through to transcript progress.

This is an internal restructuring of where loading state lives rather than a user-facing feature.