Previously `getRepoRoot` and `ensureAutoresearchBranch` only consulted `jj.isPureJjRepo` after `git.repo.root` returned null. For a jj workspace nested under an unrelated outer Git checkout, `git.repo.root` walks up and finds the outer .git, so the pure-jj branch never fired and isolation/autoresearch silently mutated the surrounding Git tree behind jj's back.
Both call sites now run the pure-jj guard first, rejecting at the jj workspace's own root regardless of any surrounding Git checkout. Added integration tests for the nested case on both surfaces.
Refs #1935