You can check inside the hook if you're in the middle of the rebase, and exit the hook early. This is what we have in our hooks: if [ -d "$(git rev-parse

You can check inside the hook if you're in the middle of the rebase, and exit the hook early. This is what we have in our hooks: if [ -d "$(git rev-parse --git-path rebase-merge)" ] || \ [ -d "$(git rev-parse --git-path rebase-apply)" ] || \ [ -f "$(git rev-parse --git-path MERGE_HEAD)" ]; then exit 0 fi