Since it's generated, it shouldn't be under version control but I'm not sure how having a primary source directory and a generated source directory would affect the Eclipse builds and setup for android. Since there were no objections, I went ahead and made the change. By default, R.Java and aidl files are now placed in target/generated-sources directory. The next step is to add support for the new platform unit tests with a Masa build.
Thanks,
Shane