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For a file SequenceControlImpl.jcs (for example), the corresponding SequenceControlImplInitializer.java file is not produced by the builder, which causes the resulting web app to fail with an error concerning control initialization. Note that if a Java suffix is used instead of JCS (SequenceControlImpl.java, for example), then everything works.
The builder does copy .jcs files to .java files in the .tmp-src folder, which are then fed to APT by the builder, so everything seems kosher in that regard, on the face of it anyway. Looking more closely at the APTTask used by the Beehive buildWebAppCore.xml build script, I see that it iterates over the various special file extensions (jcs, jcx, jws, and so on), which Pollinate does not do. Maybe that's where the bug lies?