diff --git a/generate_patches.sh b/generate_patches.sh
new file mode 100755
index 0000000..c7bdcef
--- /dev/null
+++ b/generate_patches.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+set -e
+
+mydir="$(dirname "$(realpath "$0")")"
+pushd "$mydir" > /dev/null
+
+source ./merge_helpers.sh
+
+persist_patches() {
+    local repo="$(realpath "$1")"
+    local patch_dir="$SCHILDI_ROOT/patches/$(basename "$1")"
+    if [ ! -d "$repo" ]; then
+        echo "Unknown repo: $repo"
+        return 1
+    fi
+
+    pushd "$repo"
+
+    if [ -d "$patch_dir" ]; then
+        echo "Clearing old patches..."
+        rm "$patch_dir"/*
+    else
+        echo "Creating new patch dir $patch_dir..."
+        mkdir "$patch_dir"
+    fi
+    echo "Creating new patches"
+    git format-patch -k upstream/master.. -o "$patch_dir"
+    echo "Clearing automated commits from patches"
+    find "$patch_dir" -name "*-Automatic-package.json-adjustment.patch" -exec rm {} \;
+    find "$patch_dir" -name "*-Update-version-to-*.patch" -exec rm {} \;
+    popd
+}
+
+persist_patches element-desktop
+#persist_patches element-web
+persist_patches matrix-react-sdk
+
+popd > /dev/null
diff --git a/merge_upstream.sh b/merge_upstream.sh
index b912513..a9c3352 100755
--- a/merge_upstream.sh
+++ b/merge_upstream.sh
@@ -4,57 +4,36 @@ set -e
 
 mydir="$(dirname "$(realpath "$0")")"
 
-if [ "$1" = "--checkout" ]; then
-    git_action=checkout
-    shift
-else
-    git_action=merge
-fi
-
 pushd "$mydir" > /dev/null
 
 source ./merge_helpers.sh
 
-if [ "$git_action" = "checkout" ]; then
-    # Abandon all local submodule state
-    forall_repos git reset --hard
-    git submodule update -f --recursive
-else
-    # Check branch
-    check_branch $branch
-    forall_repos check_branch $branch
+# Persist current state
+./generate_patches.sh
 
-    # Ensure clean git state
-    forall_repos check_clean_git
-fi
+# Abandon all local submodule state
+forall_repos git reset --hard
+git submodule update -f --recursive
 
 # Fetch upstream
 forall_repos git fetch upstream
 
-# Automatic reversions
-if [ "$git_action" != "checkout" ]; then
-    automatic_i18n_reversion
-    automatic_packagejson_reversion
-fi
-
-# Merge upstream
-
 # Check if specific version to merge passed
 if [ -z "$1" ]; then
     get_latest_upstream_tag
 else
     latest_upstream_tag="$1"
 fi
-forelement_repos git "$git_action" "$latest_upstream_tag"
+forelement_repos git checkout "$latest_upstream_tag"
 
 get_current_mxsdk_tags
 
 pushd "matrix-js-sdk" > /dev/null
-git "$git_action" "$current_mxjssdk_tag"
+git checkout "$current_mxjssdk_tag"
 popd > /dev/null
 
 pushd "matrix-react-sdk" > /dev/null
-git "$git_action" "$current_mxreactsdk_tag"
+git checkout "$current_mxreactsdk_tag"
 popd > /dev/null
 
 # Refresh environment
@@ -62,11 +41,9 @@ make clean
 make setup
 
 # Apply our patches
-if [ "$git_action" = "checkout" ]; then
-    #apply_patches matrix-react-sdk
-    #apply_patches element-web
-    apply_patches element-desktop
-fi
+apply_patches matrix-react-sdk
+#apply_patches element-web
+apply_patches element-desktop
 
 # Automatic adjustments
 #automatic_i18n_adjustment