You can remove a GitHub stack while keeping its pull requests open, or close the PRs when you no longer plan to merge them:

  • jj-stack unstack removes the GitHub stack while keeping its PRs and branches.
  • jj-stack cleanup --pull-request <pr> --close closes one PR and removes its unused branch, stack overview comment, and saved link between the PR and your local change.

Both commands keep your local changes. Use jj abandon separately if you also want to discard them locally.

Remove a GitHub stack

To remove the stack from GitHub while keeping its PRs open, run:

jj-stack unstack <head-change-id>
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# Remove the GitHub grouping but keep both pull requests open
❯ jj-stack unstack mysyvsqs
Removed GitHub stack #1.

The PRs remain open, with the same base branches and dependencies. You still need to merge them from the bottom up, since each PR builds on the one below it. You can review, update, or close them individually.

The local stack also stays intact. Submitting it again recreates the GitHub stack; to split it into separate stacks, first rearrange your changes with jj.

If jj-stack says the GitHub stack no longer matches your local stack, use the --stack <number> command printed in the error.

Close the PRs in your stack without merging them

First run jj-stack unstack <head-change-id> if the PRs belong to a GitHub stack. Then close and clean up each PR, starting at the top of the stack and working downward:

jj-stack cleanup --pull-request <pr> --close

The command changes the PR’s base to trunk before closing it, then removes its unused PR branch, stack overview comment, and saved link. Working from the top down frees each lower PR’s branch before you try to remove it. Review comments and revision-history comments remain on GitHub.

If you already closed the PRs through GitHub or gh pr close, run:

jj-stack cleanup <head-change-id>

This also removes their GitHub stack, so you do not need to run jj-stack unstack first.

If cleanup keeps a branch

Cleanup keeps a PR branch while another PR still uses it as its base: an open PR, or a closed PR that GitHub could still reopen. The message names that PR. Retarget an open PR to trunk. For a closed PR, either reopen and retarget it, or delete its head branch if you no longer need to reopen it. Then rerun cleanup.

A branch also stays while its GitHub stack holds an unmerged PR that cleanup leaves in place, such as an open PR. Remove that stack with jj-stack unstack before retrying cleanup. When cleanup removes every unmerged PR in a GitHub stack, it removes the stack itself.

Close an orphaned pull request

If you abandoned a submitted change with jj abandon, jj-stack list shows its PR as an orphan: a saved pull request link whose local change is gone. If other changes from that stack remain, submit those changes first so its PRs no longer depend on the orphan’s branch. Then select the orphaned PR directly to close and clean it up:

jj-stack cleanup --pull-request <pr> --close

To close and clean up every orphaned PR in the repo at once, use orphans in place of a PR number:

jj-stack cleanup --pull-request orphans --close

If the PR’s GitHub stack also holds PRs that cleanup leaves in place, first remove that stack with the jj-stack unstack --stack <number> command printed in the error. Cleanup can also keep an orphaned PR’s branch if another PR still uses it; follow the guidance above.