Ensure that we checkout the submodules before patching(Fixes #262)

scripts/build.sh

@@ -1,3 +1,7 @@
 #!/usr/bin/env bash
 
-git submodule update --init && ./scripts/applyPatches.sh && pushd Waterfall-Proxy && mvn clean package && popd
+git submodule update --init && ./scripts/applyPatches.sh
+
+if [ "$1" == "--jar" ]; then
+     mvn clean package
+fi

waterfall

@@ -5,13 +5,13 @@ case "$1" in
         scripts/rebuildPatches.sh
     ;;
     "p" | "patch")
-        scripts/applyPatches.sh
+        scripts/build.sh
     ;;
     "m" | "up" | "merge")
         scripts/mergeUpstream.sh
     ;;
     "b" | "build")
-        scripts/build.sh
+        scripts/build.sh --jar
     ;;
     "e" | "edit")
         scripts/edit.sh