diff --git a/applyPatches.sh b/applyPatches.sh
new file mode 100755
index 0000000000..27936e7368
--- /dev/null
+++ b/applyPatches.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+if [ -z "$1" ]
+then
+    echo "Please run this script again with the clean decompile sources as an argument. In most cases this will be ../work/decompile-XXXX"
+    exit
+fi
+
+nms=$1/net/minecraft/server
+cb=src/main/java/net/minecraft/server
+#clean up and rebuild
+rm -rf $cb
+mkdir -p $cb
+for file in $(/bin/ls nms-patches)
+do
+    patchFile="nms-patches/$file"
+    file="$(echo $file | cut -d. -f1).java"
+
+    echo "Patching $file < $patchFile"
+    sed -i 's/\r//' "$nms/$file"
+
+    cp "$nms/$file" "$cb/$file"
+    patch -d src/main/java/ "net/minecraft/server/$file" < "$patchFile"
+done
\ No newline at end of file
diff --git a/makePatches.sh b/makePatches.sh
index 5c0f74f406..0ebca409b4 100755
--- a/makePatches.sh
+++ b/makePatches.sh
@@ -5,13 +5,15 @@ then
     echo "Please run this script again with the clean decompile sources as an argument. In most cases this will be ../work/decompile-XXXX"
     exit
 fi
+cb=src/main/java/net/minecraft/server
+nms="$1/net/minecraft/server"
 
-for file in $(ls src/main/java/net/minecraft/server)
+for file in $(/bin/ls $cb)
 do
     echo "Diffing $file"
-    dos2unix -q $1/net/minecraft/server/$file $1/net/minecraft/server/$file
+    sed -i 's/\r//' "$nms/$file"
     outName=$(echo nms-patches/"$(echo $file | cut -d. -f1)".patch)
-    patchNew=$(diff -u $1/net/minecraft/server/$file src/main/java/net/minecraft/server/$file)
+    patchNew=$(diff -u "$nms/$file" "$cb/$file")
     if [ -f "$outName" ]
     then
         patchCut=$(echo "$patchNew" | tail -n +3)