Copy isolation backends (reflink/apfs/btrfs/zfs/block-clone/rcopy)
materialise the worktree by duplicating its `.git` verbatim. When the
parent is a linked git worktree its `.git` is a pointer file, so the
isolation shared the parent's HEAD/index/ref namespace: a task's
`git checkout`/`commit` moved the parent's branch, and the rcopy
`git worktree add` path stacked task branches in the shared namespace.
`ensureIsolation` now runs `git.detachGitDir` after `isoStart`, turning
each isolation into a standalone repo with a frozen HEAD/refs/index
snapshot that borrows the source object database via
`objects/info/alternates`. Isolated git ops stay private, every task
branch is parented on the requested base, and patch/branch capture
(`git fetch <merged>`) still resolves objects.
Fixes#6003
An intermediate commit whose net effect is already on HEAD (redundant
change, or 3-way merged to HEAD by "theirs == ours") stopped the
sequencer with "The previous cherry-pick is now empty" and was
treated as a hard conflict. mergeTaskBranches aborted the whole range,
marked the branch failed, and dropped every remaining non-overlapping
commit.
Add cherryPick.skip and cherryPick.isEmptyError to the git namespace,
then in mergeTaskBranches' catch classify the failure before aborting:
loop --skip while the error stderr matches the "now empty" phrase so
consecutive empties advance the sequencer; fall through to abort/fail
on the first non-empty error (genuine conflict with unmerged files).
Fixes#4438
mergeTaskBranches and applyNestedPatches both stashed dirty WIP, cherry-picked
task branches, then called `git stash pop` in a finally block. On conflict git
left stage 1/2/3 unmerged entries in .git/index with no MERGE_HEAD to abort;
neither call cleaned up. The corrupted index persisted indefinitely, and every
subsequent overlay-isolated task inherited it through the lower layer —
captureRepoDeltaPatch then emitted `diff --cc` (combined merge format) that
git apply rejects with "No valid patches in input", failing every downstream
task merge with 'Branch merge failed before a task branch could be created'.
Fix at the git API level: git.stash.tryPop now runs `git apply --3way --check`
on `git stash show -p --binary stash@{0}` before popping (`--3way` matches
what git stash pop does internally, so context that drifted after cherry-pick
is still accepted). Preflight failure short-circuits — stash entry preserved,
index untouched. Preflight pass falls through to pop; if pop still leaves
unmerged entries (mode-only or delete/modify conflicts the preflight can miss),
a `reset --hard HEAD" fallback restores the merged HEAD without losing the
cherry-picked commits (stash is preserved by git on failed pop, so the user's
WIP stays recoverable).
Both call sites now share this contract via git.stash.tryPop.
Fixes#4175
Tracking raw agent-commit count meant an agent that committed only its
inherited baseline WIP (via `git add -A`) then left the real edit
uncommitted collapsed every filtered patch to empty, so tmpDir never
advanced past baselineSha yet the leftover path assumed it had.
replayFilteredAgentCommits now counts filtered commits actually applied
and, when zero landed, bypasses the finalFilteredTree/leftoverPatch
synthesis entirely — writeSyntheticTree(HEAD, [rootPatch]) fails hard
whenever rootPatch has HEAD+WIP context for a file missing from HEAD's
index (untracked / staged-new WIP). Instead, commit rootPatch directly
with WIP seed, matching the no-agent-commit path.
Added regression test covering the reviewer's scenario.
captureRepoDeltaPatch records the delta against `HEAD + WIP`, so the
patch's context lines and blob SHAs reference the WIP-modified files.
commitPatchToBranchWorktree then tried to apply that patch to a fresh
worktree pinned at HEAD, which failed hard whenever the WIP-side file
was missing from HEAD's index (untracked WIP files, staged-new WIP
files) or when --3way could not resolve an overlap.
commitPatchToBranchWorktree now tries plain apply first, then `--3way`
(which cleanly subtracts WIP via the shared ODB blob for tracked files),
and only when both fail replays baseline WIP into the temp worktree so
the delta's context lines up, rewinding WIP-only files afterward so
they never leak into the branch commit.
Added git.ls.tree helper for the WIP-only-file filter and a set of
regression tests covering the untracked, staged-new, and overlap
scenarios.
Fixes#4136
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
When an isolated task agent commits its own changes before yielding, the
harness used to collapse the captured delta into one AI-summarized commit
and discard the agent's commit messages and authorship entirely. This
violated commit discipline for agentic swarms — multiple logical commits
("fix bug" + "add test") became a single opaque commit, and the
agent's commit object (which lived in isolation/.git/objects under
overlayfs/rcopy) was lost when cleanupIsolation tore down the overlay.
commitToBranch now detects when isolation HEAD moved past baseline.root
.headCommit. When it has, the function git-fetches the agent's HEAD into
the parent repo as omp/task/${taskId} so the commit objects survive
cleanupIsolation, and stamps the captured baselineSha onto the returned
CommitToBranchResult. mergeTaskBranches cherry-picks the inclusive range
baseSha..branchName when baseSha is provided, replaying each agent
commit verbatim with its original message and author. Any uncommitted
leftover (staged, unstaged, untracked) on top of the agent's last commit
becomes one trailing AI-summarized commit on the same branch.
Falls back to the legacy single-commit path when the agent never moved
HEAD (purely dirty working tree); existing patch-mode flow is untouched.
Fixes#3842
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
Used compact hashed isolation directory segments and the short m mount dir so long task ids are not copied into subagent working paths.
Kept worktree cleanup compatible with legacy merged task-isolation directories.
Fixes#3756
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
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.
- Replaced all Bun.which() calls with $which() utility from @oh-my-pi/pi-utils across 22 files.
- Removed findBashOnPath() wrapper function from procmgr.ts, consolidating binary path resolution.
- Updated AGENTS.md documentation to reflect new $which() API usage pattern.
- Centralized binary detection logic through shared utility, reducing code duplication.
- 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.
- Extracted git operations from ControlledGit class into centralized utils/git module with 1276 lines of typed command wrappers.
- Replaced dependency injection of ControlledGit instances with direct cwd string parameters across commit agent tools and workflows.
- Migrated all git command execution from inline shell calls and custom helpers to structured git module API (diff, status, branch, worktree, patch, etc.).
- Removed ControlledGit class, operations.ts, and helper functions (findGitHeadPath, mergeStdoutStderr, joinPatch) now provided by git module.
- Exported git utilities from main package entry point for extension and plugin use.
* fix: use --no-optional-locks for background git status calls
Prevent index.lock contention by adding --no-optional-locks to all
git status --porcelain calls. This is the same approach VSCode uses
in its built-in git extension (GIT_OPTIONAL_LOCKS=0).
The status-line component polls git status every ~1s to show
staged/unstaged/untracked counts. Without --no-optional-locks,
each call acquires index.lock for an opportunistic index refresh,
which blocks concurrent git operations (pull, rebase, commit) run
by the user or by omp's own tool execution.
The git-status documentation explicitly recommends this:
'Scripts running status in the background should consider
using git --no-optional-locks status'
References:
- git docs: https://git-scm.com/docs/git-status (BACKGROUND REFRESH)
- git commit adding the flag: https://github.com/git/git/commit/27344d6
- VSCode's fix: GIT_OPTIONAL_LOCKS=0 in extensions/git/src/git.ts:2716
- Claude Code same issue: https://github.com/anthropics/claude-code/issues/11005
- GitExtensions same issue: https://github.com/gitextensions/gitextensions/issues/5066
- VSCode issue #31069: https://github.com/microsoft/vscode/issues/31069
* style: fix biome formatting for long lines in worktree.ts
- Consolidated @oh-my-pi/pi-utils subpath imports into single package root import across 100+ files.
- Moved tryParseJson utility from local web scrapers module to @oh-my-pi/pi-utils package for centralized JSON parsing.
- Renamed loadSkillsFromDir to scanSkillsFromDir and refactored skill discovery to use fs.promises.readdir instead of glob-based approach.
- Replaced custom parseJSON with tryParseJson across discovery modules for consistent error handling.
- Removed emitCustomToolSessionEvent method and cleanupSshResources function, consolidating shutdown logic into dispose method.
- Updated glob pattern construction to use GlobBuilder with literal_separator(true) for improved path handling.
- Extracted directory path utilities from multiple packages into a centralized '@oh-my-pi/pi-utils/dirs' module.
- Moved 30+ path helper functions (getAgentDir, getConfigRootDir, getPluginsDir, getMCPConfigPath, etc.) from scattered locations into a single shared utility module.
- Consolidated APP_NAME, CONFIG_DIR_NAME, and VERSION constants into the centralized dirs module for reuse across packages.
- Updated 70+ import statements across packages/ai, packages/coding-agent, packages/stats, and packages/tui to use the new centralized module.
- Removed local path construction logic and replaced with utility function calls for improved maintainability and consistency.
- Deleted packages/coding-agent/src/extensibility/plugins/paths.ts as its functions were moved to the centralized dirs module.
- Migrated console.error() calls to structured logger.warn() and logger.error() throughout codebase.
- Updated os.tmpdir() import style in browser tool from destructured to namespace import.
- Replaced nanoid and randomUUID with Snowflake ID generator across codebase for consistent distributed ID generation.
- Created new Snowflake utility module in packages/utils with support for 64-bit distributed ID generation with configurable epoch, machine ID, and sequence numbers.
- Updated session ID format documentation from nanoid to snowflake hex string format (16 hex characters).
- Removed nanoid dependency from package.json as it is now replaced by internal Snowflake implementation.
- Removed Prettier configuration files (.prettierignore and .prettierrc) and migrated formatting to Biome.
- Updated Biome configuration from version 2.3.11 to 2.3.12 and changed arrowParentheses rule from 'always' to 'asNeeded'.
- Pinned @biomejs/biome dependency to exact version 2.3.12 in package.json and bun.lock.
- Applied consistent arrow function formatting across 489 files by removing unnecessary parentheses around single parameters.
- Removed blank lines after comment blocks and reorganized imports for consistency across the codebase.
- Converted named imports from node modules (fs, path, os) to namespace imports across all packages.
- Extended extension loader error handling with isEacces and hasFsCode type guards.
- Converted readdirSync, readFileSync, and statSync to async readdir, readFile, stat across skills and agent discovery.
- Made scanDirectoryForSkills async and refactored custom directory scanning to use Promise.all for concurrent processing.
- Updated agent discovery to use fs/promises for async file reading and refactored helper patterns.
- Added AgentParsingError exception class for better error handling during agent parsing.
- Added filesystem error type guards (isEnoent, isEacces, isPerm, etc.) to pi-utils for safe error checking.
- Added color manipulation utilities to pi-utils for accessibility features.
- Added color-blind mode setting to settings manager.
- Migrated plugins, settings, and config modules from sync to async file operations.
- Updated error handling to use new pi-utils type guards for type-safe checking.
roboomp