diff --git a/applyPatches.sh b/applyPatches.sh
index 21a0eb6a5..589a0cc9a 100755
--- a/applyPatches.sh
+++ b/applyPatches.sh
@@ -10,21 +10,23 @@ function applyPatch {
     branch=$3
     cd "$basedir/$what"
     git fetch
-    git branch -f upstream "$branch" >/dev/null
+    git reset --hard "$branch"
+    git branch -f upstream >/dev/null
 
     cd "$basedir"
     if [ ! -d  "$basedir/$target" ]; then
-        git clone "$what" "$target"
+        git clone $1 $target -b upstream
     fi
     cd "$basedir/$target"
     echo "Resetting $target to $what..."
-    git remote add -f upstream ../$what >/dev/null 2>&1
+    git remote rm upstream 2>/dev/null 2>&1
+    git remote add upstream ../$what >/dev/null 2>&1
     git checkout master >/dev/null 2>&1
     git fetch upstream >/dev/null 2>&1
     git reset --hard upstream/upstream
     echo "  Applying patches to $target..."
-    git am --abort >/dev/null 2>&1
-    git am --3way --ignore-whitespace "$basedir/${what}-Patches/"*.patch
+    git am --abort
+    git am --3way "$basedir/${what}-Patches/"*.patch
     if [ "$?" != "0" ]; then
         echo "  Something did not apply cleanly to $target."
         echo "  Please review above details and finish the apply then"
@@ -35,5 +37,14 @@ function applyPatch {
     fi
 }
 
-applyPatch Bukkit Spigot-API HEAD && applyPatch CraftBukkit Spigot-Server patched
-applyPatch Spigot-API PaperSpigot-API HEAD && applyPatch Spigot-Server PaperSpigot-Server HEAD
\ No newline at end of file
+echo
+echo "Applying SpigotMC patches to CraftBukkit and Bukkit"
+echo
+cd ../Bukkit
+hash=$(git rev-parse HEAD)
+git branch -f spigot "$hash"
+applyPatch Bukkit Spigot-API origin/spigot && applyPatch CraftBukkit Spigot-Server origin/patched
+echo
+echo "Applying PaperSpigot patches to Spigot-Server and Spigot-API"
+echo
+applyPatch Spigot-API PaperSpigot-API && applyPatch Spigot-Server PaperSpigot-Server
diff --git a/rebuildPatches.sh b/rebuildPatches.sh
index e5743cd14..268aef04a 100755
--- a/rebuildPatches.sh
+++ b/rebuildPatches.sh
@@ -3,19 +3,23 @@
 PS1="$"
 basedir=`pwd`
 echo "Rebuilding patch files from current fork state..."
-git config core.safecrlf false
 
 function cleanupPatches {
     cd "$1"
     for patch in *.patch; do
-        echo "$patch"
         gitver=$(tail -n 2 $patch | grep -ve "^$" | tail -n 1)
-        diffs=$(git diff --staged $patch | grep -E "^(\+|\-)" | grep -Ev "(From [a-z0-9]{32,}|\-\-\- a|\+\+\+ b|Date\: |.index)")
+        diffs=$(git diff --staged $patch | grep -E "^(\+|\-)" | grep -Ev "(From [a-z0-9]{32,}|\-\-\- a|\+\+\+ b|.index)")
 
         testver=$(echo "$diffs" | tail -n 2 | grep -ve "^$" | tail -n 1 | grep "$gitver")
         if [ "x$testver" != "x" ]; then
-            diffs=$(echo "$diffs" | sed 'N;$!P;$!D;$d')
+            mingw=$(uname -s | grep "MINGW")
+            if [ "x$mingw" != "x" ]; then
+                diffs=$(echo "$diffs" | head -n $(($(echo "$diffs" | wc -l | sed -r 's/^ +//' | cut -d ' ' -f 1) - 2)))
+            else
+                diffs=$(echo "$diffs" | head -n -2)
+            fi
         fi
+        
 
         if [ "x$diffs" == "x" ] ; then
             git reset HEAD $patch >/dev/null
@@ -27,16 +31,15 @@ function cleanupPatches {
 function savePatches {
     what=$1
     target=$2
-    echo "Formatting patches for $what..."
     cd "$basedir/$target"
-    git format-patch --no-stat -N -o "$basedir/${what}-Patches/" upstream/upstream >/dev/null
+    git format-patch --no-stat -N -o "$basedir/${what}-Patches/" upstream/upstream
     cd "$basedir"
-    git add -A "$basedir/${what}-Patches"
+    git add "$basedir/${what}-Patches"
     cleanupPatches "$basedir/${what}-Patches"
     echo "  Patches saved for $what to $what-Patches/"
 }
-if [ "$1" == "clean" ]; then
-	rm -rf Spigot-*-Patches
-fi
+
+#savePatches Bukkit Spigot-API
+#savePatches CraftBukkit Spigot-Server
 savePatches Spigot-API PaperSpigot-API
-savePatches Spigot-Server PaperSpigot-Server
\ No newline at end of file
+savePatches Spigot-Server PaperSpigot-Server