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Hi Mike, unfortunately, as you've found, the modules support in Flex Builder is not quite there yet. There are two ways to do it:
1) Create a separate project for each module.
2) Add modules to an existing project.
For #1: You can create a new project for each module. Turn off the HTML wrapper and change the output folder to a folder that the main project will look at to get the modules.
For #2: You can add modules as applications as long as they are in the same directory as the main application file. If you try to put them in sub directories, you won't be able to automatically compile them in Flex Builder. In that case, you can compile them separately into a sub directory with the command line compiler.
I will be enhancing the modules documentation to include Flex Builder issues in the very near future.
Thanks for the overview, I would like to clarify a few things...
On option one a project for each module, this actually seems to make sense because you could change one module at a time and recompile. I believe I successfully placed two modules in one second project so for groups of modules this seems to make sense.
With that said, what about the -link-report=report.xml how would you configure this on that module project to reference the main app project?
I am using Link Type=External, for some of my class libraries, but I don’t think that is the same as link-report=report.xml, which sounds more like it looks at main app making sure you don’t load anything twice?