# Move\_agent\_to\_root fails after deleted remote branch: Failed to checkout migrated branch / couldn't find remote ref **URL:** \ **Category:** Bug Reports\ **Tags:** mcp, worktrees\ **Created:** [July 9, 2026, 3:01pm UTC](https://forum.cursor.com/t/move-agent-to-root-fails-after-deleted-remote-branch-failed-to-checkout-migrated-branch-couldnt-find-remote-ref/165298 "2026-07-09T15:01:01Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![jsolly](https://sea3.discourse-cdn.com/cursor1/user_avatar/forum.cursor.com/jsolly/32/33752_2.png) [@jsolly](https://forum.cursor.com/u/jsolly)\ **Post date:** [July 9, 2026, 3:01pm UTC](https://forum.cursor.com/t/move-agent-to-root-fails-after-deleted-remote-branch-failed-to-checkout-migrated-branch-couldnt-find-remote-ref/165298/1 "2026-07-09T15:01:01Z")
### Where does the bug appear (feature/product)? Cursor IDE ### Describe the Bug cursor-app-control → move\_agent\_to\_root hard-fails when Cursor tries to check out a **migrated branch that no longer exists on the remote** (typical after merge + delete-branch + worktree cleanup). Verbatim UI error: ```auto Failed to move agent root: Failed to checkout migrated branch "feat/github-actions-templates": Command failed: git fetch origin refs/heads/feat/github-actions-templates:refs/remotes/origin/feat/github-actions-templates --no-tags --recurse-submodules=no --no-write-fetch-head fatal: couldn't find remote ref refs/heads/feat/github-actions-templates ``` This is a different failure mode from the existing worktree-checkout conflict report ([Move\_agent\_to\_root MCP fails in git worktrees](https://forum.cursor.com/t/move-agent-to-root-mcp-fails-in-git-worktrees/159576)) — that one fails with “branch is already used by worktree”. Here the branch is **gone from origin** , and migration still insists on fetching it by name. ### Evidence 1. **Branch lifecycle was normal.** PR merged and remote branch deleted: 2. **Cursor still binds the agent/workspace to the deleted path.** workspaceStorage/…/workspace.json still contains folder pointing at that missing worktree. On this machine there are **39** workspaceStorage entries whose folder paths are missing (mostly cleaned-up worktrees). 3. **Same class of git failure for another deleted branch the same day** (vscode.git log): ```auto 2026-07-09 09:43:46.920 [info] > git fetch origin fix/live-provider-premarket-quotes [491ms] 2026-07-09 09:43:46.920 [info] fatal: couldn't find remote ref fix/live-provider-premarket-quotes ``` Also earlier at 08:49 / 08:50 for the same branch. 1. While the worktree still existed, git logs for that workspace show healthy activity on feat/github-actions-templates (window1\_wb4, workspaceId 695ee29de232dd3a965e3ee427e69624). After cleanup, migration still targets that branch name. 2. Tool description for move\_agent\_to\_root says it will fetch/ff-merge the destination; the failure path appears to treat the agent’s remembered branch as mandatory even when the destination path is gone / branch deleted. ### Steps to Reproduce 1. From an empty-window / home agent, create a linked worktree on a feature branch and call move\_agent\_to\_root to that worktree path. 2. Push, merge the PR, delete the remote branch, remove the worktree (git worktree remove + git branch -d). 3. Optionally call move\_agent\_to\_root back to the primary checkout (this was attempted in the session; Cursor still retained the old workspace binding). 4. Later, reopen the agent chat or otherwise trigger workspace-root migration for that conversation. 5. Observe: Failed to move agent root: Failed to checkout migrated branch “” with git fetch … fatal: couldn’t find remote ref. ### Expected Behavior If the migrated branch is missing on the remote (and/or the remembered worktree path no longer exists), move\_agent\_to\_root should: - fall back to the requested rootPath / primary checkout without requiring that branch, or - clear/update the stale workspace binding and move successfully to an existing path, instead of hard-failing the entire move on a deleted remote ref. ### Operating System MacOS ### Version Information Version: 3.10.20 VSCode Version: 1.125.0 Commit: 23b9fb205fe595ea2be29da7214e19762d037fc0 Date: 2026-07-07T07:03:33.071Z Layout: glass Build Type: Stable OS: Darwin arm64 25.5.0 (macOS 26.5.2) ### For AI issues: which model did you use? Grok 4.5 (Cursor agent) ### For AI issues: add Request ID with privacy disabled investigation: 6862686e-d555-49cb-b430-562ddf710d3f worktree session that created/moved to the branch: 80bcb98c-7f32-42c9-adca-96f838c0ee64 (Data sharing enabled) ### Why this shows up for power-user / worktree workflows This is likely uncommon for users who open one folder and stay there. My agent setup manufactures the exact lifecycle that trips the bug: 1. **Worktree-first authoring** — local rules require change-making work in a git worktree off `main` (enforced by a write guard that blocks edits on a `main` checkout). 2. **Home / empty-window → `move_agent_to_root`** — Cursor home-workspace guidance + `cursor-app-control` MCP instruct the agent to call `move_agent_to_root` once the worktree/project path is known, so the conversation binds to that disposable checkout. 3. **Early worktree cleanup** — after PR open (fire-and-forget ship), the worktree is removed at PR creation, not after merge. 4. **Delete head branches on merge** — GitHub `delete_branch_on_merge=true` removes the remote ref once the PR lands. Cursor still remembers the migrated branch / workspace path after (3)+(4). Reopen or remigrate → `git fetch` of a deleted ref → hard fail. On this machine that pattern is heavy (~30 workspace bindings to worktrees; ~39 `workspaceStorage` entries pointing at missing paths). Same class of failure the same day for another deleted branch (`fix/live-provider-premarket-quotes`). So: not a weird git config — high-churn agent + worktree + ship-cleanup + delete-on-merge. Cursor’s move logic doesn’t handle “that branch is gone” yet. ### Additional Information Related: closest cousin (different error) [Move\_agent\_to\_root MCP fails in git worktrees](https://forum.cursor.com/t/move-agent-to-root-mcp-fails-in-git-worktrees/159576) — branch already used by worktree / hang variants. Mohit noted broader worktree migration gaps. No exact match found for “Failed to checkout migrated branch” + “couldn’t find remote ref” after merge/delete. Workaround: Open the primary repo with File → Open Folder and start a fresh chat there. Avoid reopening agent chats rooted in deleted worktrees. Pruning stale origin/\* refs does NOT stop the failure (Cursor fetches the branch by name from remembered state). Logs attached: [cursor-move-agent-root-deleted-branch-20260709.zip](https://forum.cursor.com/uploads/short-url/fMqDntRD4qFDkmu9pcsh7wlkh9e.zip) (74.6 KB) — vscode.git excerpts + workspace/git evidence; emails redacted. Happy to pull more windows if useful. ### Does this stop you from using Cursor Sometimes - I can sometimes use Cursor ---
**Author:** ![mohitjain](https://sea3.discourse-cdn.com/cursor1/user_avatar/forum.cursor.com/mohitjain/32/100229_2.png) [@mohitjain](https://forum.cursor.com/u/mohitjain)\ **Post date:** [July 10, 2026, 7:34am UTC](https://forum.cursor.com/t/move-agent-to-root-fails-after-deleted-remote-branch-failed-to-checkout-migrated-branch-couldnt-find-remote-ref/165298/7 "2026-07-10T07:34:07Z")
Hey @jsolly, thanks for the write-up. This is a real bug. When move\_agent\_to\_root migrates onto a branch that was merged and deleted from origin, the migration still fetches that branch by name and hard-fails on `couldn't find remote ref` instead of falling back. We’ve seen this deleted/merged-branch migration failure before and the team is actively hardening this path. I don’t have a timeline, and it isn’t fixed on stable yet, so your workaround is the right call for now: open the primary repo with File → Open Folder and start a fresh chat there, rather than reopening agent chats rooted in deleted worktrees. I’ve logged your report and repro with the team tracking this. Thanks again for the detail.