The following is a sample content of the <Deployment Unit Object Name>_user.gxdproj file that is used to add additional files or exclude files from a Deployment using Application Deployment tool
<?xml version="1.0" encoding="utf-8"?>
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<PropertyGroup>
<AdditionalDirectory>c:\MyAdditionalFiles\</AdditionalDirectory>
</PropertyGroup>
<ItemGroup>
<!--AdditionalFile Include="some File to copy"/-->
<!--
This file will be copied to $(DeployFullPath)\$(AdditionalFileDestination)
<AdditionalFile Include="C:\myfiles\myfile.txt"/>
This file will be copied to $(DeployFullPath)\TargetDir
<AdditionalFile Include="C:\myfiles\my other file.txt">
<RelativeTargetDir>TargetDir</RelativeTargetDir>
</AdditionalFile>
-->
<!-- Add files that you dont want in your destination folder or war/jar/zip file
<ExcludeFile Include="myfile.txt"/>
-->
</ItemGroup>
</Project>
All the content (files and subfolders) specified in AdditionalDirectory will be copied to the root of the application (maintaining its structure)
Every AdditionalFile, on the other hand, will be copied to the root of the application unless specified otherwise by the RelativeTargetDir property.