Migrate 203 test files (356 call sites) from fs.rm/fs.rmSync to
removeWithRetries/removeSyncWithRetries to reduce EBUSY test failures
on Windows. removeWithRetries is now exported from @oh-my-pi/pi-utils.
The migration uses a regex-based approach that:
- Replaces fs.rm(path, { recursive, force }) → removeWithRetries(path)
- Replaces fs.rmSync(path, { recursive, force }) → removeSyncWithRetries(path)
- Replaces fs.rm(path) → removeWithRetries(path) (no options)
- Skips fs.rm/fs.rmSync inside template literals (bun --eval scripts)
- Adds imports to existing @oh-my-pi/pi-utils import or creates new one
- Removes unused fs imports where fs.rm was the only fs usage (4 files)
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
Resolves conflict in test/task/worktree.test.ts by keeping both the
getRepoRoot (main) and applyNestedPatches (PR) describe blocks.
Extends the PR's Python/JS work to the remaining workflow runtimes:
- eval/rb/prelude.rb, eval/jl/prelude.jl: agent() now accepts and
forwards isolated/apply/merge (as booleans) plus returnHandle, and the
return_handle node carries isolated/patch_path/branch_name/
nested_patches/changes_applied/isolation_summary.
Post-merge fixups:
- task/index.ts: drop dead commitStyle var (the dedup refactor reads
task.isolation.commits inside makeIsolationCommitMessage).
- CHANGELOG: move the misplaced Added entry under [Unreleased], correct
the stale "defaults track task.isolation.mode" wording to the final
strict opt-in behavior, and note all four runtimes.
Fixes#3196
git stash pop without --index restores stashed staged changes as unstaged. When a nested repo had staged WIP before the isolated agent ran, the pop in applyNestedPatches() brought the content back but lost the user's index state.
Pass { index: true } so pop uses --index, matching the root merge path that already does the same thing.
Added a regression test that stages a pre-existing edit in the nested repo, runs applyNestedPatches, and asserts the file is still in the index (porcelain "M " with the trailing space) and the cached diff still shows the staged WIP.
Fixes#3196
applyNestedPatches() applied the captured patch then ran git.stage.files(nestedDir), which stages every working-tree change in the nested repo. A nested repo that was already dirty before the agent ran ended up with the user's unrelated work-in-progress committed alongside the agent delta.
Stash any pre-existing dirty state (tracked + untracked) before applying the patch and pop it back in the finally block after the commit, so the agent commit contains only the captured patch and the user's in-flight work is restored on top of it. A failing stash pop logs a warning and leaves the stash entry intact for manual recovery; the broader nested-apply failure path is already non-fatal.
Added a worktree integration test that confirms a pre-existing untracked file in the nested repo is not staged into the agent commit and is still present in the working tree afterwards.
Fixes#3196
- Replaced Bun.sleep and wall-clock timing with fake timers (vi.useFakeTimers), release gates, and deterministic polling across 15+ test files to eliminate flakiness and improve speed.
- Consolidated per-test fixture setup into beforeAll/afterAll lifecycle hooks across 20+ test files, reducing redundant initialization and improving test performance by reusing shared immutable fixtures.
- Stubbed network calls in ModelRegistry and test discovery to prevent unintended outbound requests during test execution.
- Replaced subprocess-based test coordination (file markers, Bun.sleep polling) with in-memory fakes (FakeWebSocket, FakeLspServer, VirtualClock) for deterministic, fast test execution.
Previously `isPureJjRepo` returned true whenever the resolved jj and git roots merely differed. That punishes the legitimate inverse-nesting case: a real git checkout (vendored repo, fixture, independent nested checkout) living UNDER an outer pure jj workspace. Both `jj.repo.root` and `git.repo.root` walk upward from cwd and return the closest ancestor — so the deeper root is the one the user is actually working inside, and Git automation against the inner checkout never touches the surrounding jj tree.
`isPureJjRepo` now returns true iff jj is the *deeper* ancestor (or no git is present at all). The new `isStrictDescendant` helper does the depth check via `path.relative`. Added unit + integration tests covering both nesting directions on all three surfaces (`utils/jj`, `task/worktree`, `autoresearch/git`).
Refs #1935
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
Worktree setup and autoresearch Git prep silently misbehaved in pure Jujutsu workspaces (`.jj/repo/` present, no colocated `.git/`):
- `task/worktree.ts#getRepoRoot` threw a generic "Git repository not found for isolated task execution.", giving a jj user no hint about what was wrong.
- `autoresearch/git.ts#ensureAutoresearchBranch` returned a soft "Not in a git repository" warning, letting `/autoresearch` proceed with no branch isolation, baseline reset, or auto-commits.
Both paths now detect a pure jj workspace via a new `jj.isPureJjRepo` helper and surface an actionable Jujutsu-specific error pointing at `jj git init --colocate`. Colocated jj-git workspaces (both `.jj/` and `.git/` at the same root) and plain Git checkouts behave exactly as before.
Fixes#1935
- Added untracked worktree baseline capture via `untrackedPatch` and synthetic tree diffing.
- Added fallback-aware backend ordering by collecting host candidates and retrying alternates on unavailable PAL.
- Hardened overlay mount lifecycle by removing stale overlays and deleting upper/work dirs after unmount.
- Refined ZFS clone deletion to validate ownership and remove dataset+origin only when checks pass.
- Updated ProjFS integration to use extended-info callbacks and symlink metadata reads.
- Updated rcopy path handling to absolutize paths, and added `writeTree` plus combined shell timeout checks.
- Added unified isolation primitives (BackendKind, ProbeResult, IsoError) and resolve fallback selection logic.
- Added Diff, FileChange, and ChangeKind with default_diff choosing git mode or filesystem walk based on repository state.
- Added APFS/btrfs/zfs/reflink/overlayfs/projfs/rcopy/block-clone backends with platform-aware start, stop, and probe.
- Mapped backend operations to canonicalized paths, recursive clone helpers, rollback cleanup, and unavailable error mapping.
- Added unified native exports isoBackend/isoProbe/isoResolve/isoStart/isoStop/isoDiff and removed projfsOverlay APIs.
- Replaced task isolation resolver flow with ensureIsolation/cleanupIsolation and migrated mode handling to auto plus legacy-mode aliases.
- Fixed memory leak by cancelling idle compaction timer on event controller disposal.
- Fixed session resumption to preserve last non-empty session when starting fresh.
- Fixed stash detection to use git ref resolution instead of output parsing for reliability.
- Fixed secret obfuscation to deobfuscate restored session messages locally while keeping LLM messages obfuscated.
- Fixed stash pop operation to preserve staged changes with --index flag after task branch merges.
- Changed idle compaction settings from enum to numeric type for flexible configuration.
oldschoola