diff --git a/Makefile b/Makefile
index 1e66999ba..39d9ff2ea 100644
--- a/Makefile
+++ b/Makefile
@@ -119,17 +119,17 @@ tfgen: install_plugins upstream
 
 upstream:
 ifneq ("$(wildcard upstream)","")
-	@$(SHELL) ./scripts/upstream.sh "$@" apply
+	scripts/upstream.sh "$@" apply
 endif
 
 upstream.finalize:
-	@$(SHELL) ./scripts/upstream.sh "$@" end_rebase
+	scripts/upstream.sh "$@" end_rebase
 
 upstream.rebase:
-	@$(SHELL) ./scripts/upstream.sh "$@" start_rebase
+	scripts/upstream.sh "$@" start_rebase
 
 bin/pulumi-java-gen:
-	$(shell pulumictl download-binary -n pulumi-language-java -v $(JAVA_GEN_VERSION) -r pulumi/pulumi-java)
+	pulumictl download-binary -n pulumi-language-java -v $(JAVA_GEN_VERSION) -r pulumi/pulumi-java
 
 # To make an immediately observable change to .ci-mgmt.yaml:
 #
diff --git a/scripts/upstream.sh b/scripts/upstream.sh
old mode 100644
new mode 100755
index c455b4655..84f57d7b1
--- a/scripts/upstream.sh
+++ b/scripts/upstream.sh
@@ -1,3 +1,4 @@
+#!/usr/bin/env bash
 # WARNING: This file is autogenerated - changes will be overwritten if not made via https://github.com/pulumi/ci-mgmt
 
 set -e
@@ -163,8 +164,11 @@ EOF
 # It is used to make the error message more actionable.
 end_rebase() {
   assert_rebase_in_progress "$1"
+  # Use git to resolve the possible location of files indicating a rebase might be in progress.
+  rebase_merge_dir=$(cd upstream && git rev-parse --git-path rebase-merge)
+  rebase_apply_dir=$(cd upstream && git rev-parse --git-path rebase-apply)
 
-  if [ -d .git/modules/upstream/rebase-merge ]; then
+  if [[ -d "${rebase_merge_dir}" || -d "${rebase_apply_dir}" ]]; then
     echo "rebase still in progress in './upstream'. Please resolve the rebase in"
     echo "'./upstream' and then run 'make \"$1\"' again."
     exit 1
@@ -172,8 +176,10 @@ end_rebase() {
 
   rm patches/*.patch
   cd upstream
-  git format-patch local -o ../patches
-  rm ../rebase-in-progress
+  git format-patch local -o ../patches --no-prefix --zero-commit --no-signature --no-stat
+  cd ..
+  rm rebase-in-progress
+  apply "$1"
 }
 
 case $2 in