I think I stumbled upon a bug in Flash Builder 4.6. I'm running FB on OSX 10.7 and I'm building native extension for OSX (AIR 3.1).
After successfull creation of my extension's native code .framework file in Xcode, writing Action Script wrapper around it and packaging everything together in ANE file (using adt) I discovered that I couldn't start a debug session from Flash Builder (4.6 and AIR 3.1). Since I was able to test my extension from terminal (using adl), I am pretty sure that I connected all the dots correctly.
I discovered that Flash Builder only before starting debug session unpacks the extension's .ane file into some temporary folder, beneath the workspace. Unfortunately, it messes the attributes of unpacked files so aliases are missing (they look like regular files) and main binary inside OSX's .framework package is missing executable attribute. Since those aliases and attributes are essential for things to work on OSX, FB simply fails to find extension and reports error like "ArgumentError: Error #3500: The extension context does not have a method with the name". Somebody else stumbled upon this in following post http://forums.adobe.com/message/3974973 (it seems it's specific to Linux and OSX, but not Windows - no aliasing there, huh?).
I would appreciate if somebody from Adobe could check that and verify if that's up to Flash Builder or not.
Thanks