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When I got the message "can't use declare parents to change superclass of binary form ... (implementation limitation)", I added the source file to the compile but still got the message. It would be nice if binary limitations did not apply when source files are provided, even if the .class file is also on the inpath, to reduce the changes to the build process required to work around this limitation.
I believe all binary limitations are now removed, in order to fully support incremental compilation (which runs in binary mode most of the time).
Verified with latest CVS that you can declare parents on binary class. Created another bug 88776: ajc should not prefer source to binary but should issue an error on duplication, as it does for duplicate classes in source form. (This has the potential to break existing build scripts that rely on ajc silently ignoring duplicates.)