Is it possible to set the root folder/package of the generated code and location of assets/component? Right now, catalyst drops all the resources & components right under the /src folder, which of course is unpractical when i tried to bring a catalyst component into my existing project folder structure. I had to manually move all the resources & components to the right package and fix all the Embed Image and SWF directives in the generated MXML. If you could set Catalyst to drop all the resources & components to like org.somedomain.someapp.mainmenu package instead of just the root, and use image urls realtive to that folder it could really speed up the process of integrating the design with the application code and not cause name conflicts between various components.
Unfortunately, there's no option to configure the various directories we create.
If you use current builds, the situation should be a little better than you described. All assets go into the "assets" folder, and all components go into a "components" folder.
This is on our enhancement request list.