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I think the simplest way to work with Flex, Java, and LCDS in Eclipse is by creating an Eclipse Java project and then adding a Flex Project to it. This will let you work in the single project and use the Flash perspective (Flash Builder) for your LCDS client code and the Java perspective for your  Java code. I don't think you need to go the WTP route. You DO need to use the Flash Builder plug-in rather than Flash Builder stand-alone.

Here's the basic process:

1. Create a Java project in Eclipse.

2. In your Java project, you can optionally set the output location to be a linked directory in your LCDS web app. For example, maybe you want to save POJO classes in the WEB-INF/classes directory of your web application. This is an option when you configure the source and output directories for your project:

  - Select the Allow Output Folders For Source Folders option when configuring your project.

  - Select Browse next to the Default Output Folder field.

  - Select the project directory name. Select Create New Folder.

  - Select Advanced > Link To Folder In File System.

  - Browse to the location where you want to save output and click OK.

Similarly, if you will be exporting your output to a JAR file, you can save the JAR file to the WEB-INF/lib directory of your LCDS web application.

3. In the Package Explorer, right click the name of your new Java project, and select Add/Change Project Type and then select Add Flex Project.

4. Set up your Flex J2EE/LCDS project just as you normally would.

Now when you toggle between the Java and Flash perspectives, you can work on your Java and Flex code in the same project. When you build your Java project, the output will go in whatever output directory you defined, such as lcds_root/tomcat/webapps/lcds-samples/WEB-INF/classes.

The Using LCDS doc describes how you can also link your config files into your Flex project to make it easy to define your destinations, etc. from Flash Builder. It is covered here:

http://help.adobe.com/en_US/LiveCycleDataServicesES/3.1/Developing/WSc3ff6d0ea77859461172e0811f00f6e...