Dirty isolated baselines can be accidentally committed by subagents that run git add -A. Fetching the raw isolation HEAD then cherry-picking the range would replay that baseline WIP into parent history.
Add a dirty-baseline replay path that rewrites each agent commit against the captured baseline tree, preserving the agent commit message and author while excluding staged, unstaged, and untracked changes that existed before isolation started. Clean baselines still use the raw git fetch path, and nested-only changes keep returning patches without creating an empty root branch.
Add a regression for baseline staged + untracked WIP committed by the agent, asserting the task branch contains only the agent file and parent WIP remains staged/untracked after merge.
Fixes#3842
roboomp
d120ba6b7d