Keep still-running shell calls in later subagent scans

Each scan advanced the subagent's scan position to the end of its transcript, past the line that issued a still-running shell call. Later scans skipped that call, so files a long-running command (a build, an install) wrote after the first scan were counted as user work.

Tool call windows now record their issuing line, and a scan stops its position before the earliest still-running write-looking shell call, so the call is read again until its result arrives.