Use git apply --3way for patch-mode isolated merge checks and applies so diff-tree patches that are already present are accepted as no-ops.
Added regression coverage for a clean already-applied binary/full-index patch.
Fixes#4135
Applied isolated branch patches with three-way fallback when unrelated parent dirt appears in patch context.
Surfaced branch preparation failures instead of reporting no changes.
Fixes#3841
Two Codex P2 findings landed against 978d2a76d0 that were not in the previously delivered review event:
1) prepareIsolationContext() (which runs captureBaseline → walks nested repos and untracked diffs) was running OUTSIDE withBridgeTimeoutPause; on dirty/large repos the baseline walk can exceed the eval idle timeout while the runtime is blocked. Moved the prep call into the pause closure so the watchdog is suspended for the whole bridge call from prep through cleanup.
2) applyNestedPatches() swallowed git stash pop failures with only a logger.warn, so a stash-pop conflict after a successful agent commit was invisible to the workflow. Changed the helper to return Promise<string[]> of warnings; applyEligibleNestedPatches now wraps them in a <system-notification> appended to the merge summary so the caller actually sees the partial-success case.
Added regression tests:
- bridge: prepare fires after timeout-pause and before timeout-resume.
- runner: applyEligibleNestedPatches surfaces stash-restore warnings as a system-notification.
- worktree (real git): a pre-existing dirty edit on the same file the agent patches causes stash pop to conflict; the helper returns a warning naming the nested repo and the stash entry is preserved for manual recovery.
Fixes#3196
TaskTool and the eval agent() bridge each held a private copy of the nested-repo patch eligibility gate and the AI commit-message factory; isolation policy could drift between the two callers.
Moved both into task/isolation-runner.ts:
- applyEligibleNestedPatches(opts) — single nested-patch gate (skip on patch-mode parent failure, skip on branch-mode unmerged root, fail non-fatally with a system-notification suffix).
- makeIsolationCommitMessage(session) — single factory that yields the AI commit-message callback when task.isolation.commits === "ai" and a model registry is wired, undefined otherwise.
Both call sites now invoke the helpers; behavior is unchanged. Removed the now-dead generateCommitMessage/applyNestedPatches imports from each caller.
Added unit tests for the new helper covering the skip-on-patch-failure, skip-on-unmerged-branch, success, and failure-suffix paths.
Fixes#3196
Eval preludes now forward returnHandle to the bridge so no-session eval runs can preserve the temp artifacts backing returned agent:// handles. The bridge keeps those temporary artifact directories whenever returnHandle is requested, including non-isolated runs and successful isolated applies.
Branch-mode isolation now treats nested-only changes as merge-eligible even when no root branch was produced, letting callers apply nested patches instead of dropping them when the root repo had no diff.
Added regression coverage for returnHandle artifact preservation and nested-only branch isolation.
Fixes#3196
roboomp