Add submodules and build scripts

These will be made default in 1.9, dropping PaperTools support

newApplyPatches.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+PS1="$"
+basedir=`pwd`
+echo "Rebuilding Forked projects.... "
+
+function applyPatch {
+    what=$1
+    target=$2
+    branch=$3
+    cd "$basedir/$what"
+    git fetch
+    git branch -f upstream "$branch" >/dev/null
+
+    cd "$basedir"
+    if [ ! -d  "$basedir/$target" ]; then
+        git clone "$what" "$target"
+    fi
+    cd "$basedir/$target"
+    echo "Resetting $target to $what..."
+    git remote add -f upstream ../$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/${what}-Patches/"*.patch
+    if [ "$?" != "0" ]; then
+        echo "  Something did not apply cleanly to $target."
+        echo "  Please review above details and finish the apply then"
+        echo "  save the changes with rebuildPatches.sh"
+        exit 1
+    else
+        echo "  Patches applied cleanly to $target"
+    fi
+}
+
+applyPatch Bukkit Spigot-API HEAD && applyPatch CraftBukkit Spigot-Server patched
+applyPatch Spigot-API PaperSpigot-API HEAD && applyPatch Spigot-Server PaperSpigot-Server HEAD