Regarding building (ant) and debugging Flex components (Flex Builder)

I am fairly new to graniteds + flex. The example articles on graniteds and blazeds use two separate applications i.e., using mxml components and actionscripts in another project. Why is this done so?
It was hard to build the swf files in a separate project as the antscript needed something more.
<mxmlc....>
<source-path path-element="${basedir}/src"/>
</mxmlc ..>
The source here is the actual java source code. Unless I had the two projects together, I could not build the swf files. However, once I convert this one application to a java project, as flex project does not recognize java source code, I can no longer debug my flex screens. Am I missing something here?
Help
Krishna

No suggestions yet?
Could someone tell me if I could integrate these in one place atleast, if so how do we configure the application to be able to debug Flex applications?
Thanks
Krishna

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