How I set up the project: 1. I didn't merge the SDKs, instead I imported from both locations the libraries I needed. 2. My eclipse workspace contains a lot of settings (mostly syntax highlighting), that I don't want to loose, and it's in an entirely different place from where I check the source code. I.e. ~/projects/workspace and flex goes into ~/projects/flex/SDK/apache/ thus the settings in the project files from the SVN don't reflect it.
But, to be honest, I didn't even try to use them, I discovered the files later when looking through the source code. But then again, so far this isn't going to be in the actual SDK, I don't care, because it doesn't affect me. I only hope it won't affect anyone later / no special role will be assigned to those files. Best. Oleg