Interactive mode: don't start the timer for the command timeout until the user made a decision

The problem:

When in interactive mode, the user can wait more than the default timeout before choosing to start the command.
The markdown-runner tool shouldn't fail because the command did timeout before it has actually started.

No files, tests, or entry points are named. Locate the interactive-mode handling and command-timeout logic first; done means waiting before the user's decision does not trigger the timeout, while the timeout still applies after the command starts.

Written by the indexing model from the issue text.