The following build.xml doesn't produce MSI in the destination folder.

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project xmlns:fx="javafx:com.sun.javafx.tools.ant" default="fx-deploy">
    <taskdef classpath="C:\Program Files\Java\jdk1.8.0_40\\lib\ant-javafx.jar" resource="com/sun/javafx/tools/ant/antlib.xml" uri="javafx:com.sun.javafx.tools.ant"/>
    <target name="fx-deploy">
        <fx:deploy nativeBundles="msi" outdir="C:\Users\user1\AppData\Local\Temp\testBundlerWorkDir4320380386130688233" outfile="test" verbose="true">
            <fx:resources>
                <fx:fileset dir="C:\Users\user1\AppData\Local\Temp\testBundlerWorkDir4320380386130688233\jars" includes="rmApp.jar"/>
            </fx:resources>
            <fx:platform/>
            <fx:preferences/>
            <fx:application/>
            <fx:info>
                <fx:association description="The sample description" extension="foo bar" mimetype="application/example"/>
                <fx:association extension="baz qux" icon="C:\work\appBundlerTests-8u40\build\classes\com\oracle\appbundlers\utils\resources\icon2.ico" mimetype="hello/world"/>
            </fx:info>
            <fx:bundleArgument arg="mainJar" value="rmApp.jar"/>
            <fx:bundleArgument arg="classpath" value="rmApp.jar"/>
        </fx:deploy>
    </target>
</project>