How to fix fatal: It seems that there is already a rebase-apply directory in Git

First, understand what state Git is in by running:

git status

This will tell you if a rebase is in progress, if there are conflicts to resolve, and what branch you're on. Look for messages like "rebase in progress" or "You are currently rebasing".

If you have previously resolved the merge conflicts or want to continue where you left off:

git rebase --continue

If there are still unresolved conflicts, Git will tell you which files need attention. Open each conflicted file, resolve the markers (<<<<<<<, =======, >>>>>>>), then stage the resolved files with git add <filename> before running --continue again.

If you don't want to continue the rebase and prefer to start fresh:

git rebase --abort

This will cleanly undo the rebase operation, restore your branch to its state before the rebase started, and remove the .git/rebase-apply directory.

If the current commit is causing issues and you want to skip it entirely:

git rebase --skip

Use this with caution—the skipped commit's changes will not be included in your rebased branch. This is useful when the commit is already applied or creates an empty patch.

If you see "It looks like git am is in progress" when trying to abort:

git am --abort

The git am command is used to apply patches from mailbox files, and it uses the same .git/rebase-apply directory. Abort it first, then you can proceed with your intended operation.

If none of the above commands work and you're certain you want to abandon the rebase:

rm -rf .git/rebase-apply

Warning: Only do this if the standard abort commands fail. This forcefully removes the rebase state without any cleanup. After running this, verify your repository is in a good state with git status and git log.