diff --git a/.prepare b/.prepare
deleted file mode 100644
index 2b459f91e..000000000
--- a/.prepare
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-git checkout --recurse-submodules experimental
diff --git a/StanHeaders/.prepare b/StanHeaders/.prepare
new file mode 100644
index 000000000..f489db403
--- /dev/null
+++ b/StanHeaders/.prepare
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+git checkout experimental
+cd inst/include/upstream && git checkout develop && git pull && cd ../../..
+cd inst/include/upstream/lib/stan_math && git checkout develop && git pull && cd ../../../../..