- 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.
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