For what it's worth, when I was doing docs for pegasus, I could not find a single project that actually used the asdoc ant task. I looked at four or five and every one called out to Java tool instead via the java task (this is what I ended up doing as well) or exec. I think the issue was around the broken behavior of filesets or something like that, but I don't remember any details (nor the Flex version I last tried on, but I believe it was 4.5). Are there non-trivial examples of working asdocs via the ant tasks out there? If you have spare time to throw at this, I have a brief (and somewhat bitter--sorry) comment about it here: https://github.com/deafbybeheading/pegasus/blob/master/build.xml#L93
If you're not willing to dig through this, but are still interested in fixing the task (if there's still an issue), I can try to convert this back into the task version and see if it's still broken.
