Ant is actually supposed to build sources from the src directory. It builds classes from them and puts those classes into the build directory, then packages up those into the war file. You should never upload class files, as those should be rebuilt by the ant script on hurricane. If you upload your class files you are including classes built on your own machine in the war, which may be a different jdk than hurricane's.
This means NEVER, EVER check in your build directory to SVN. To ensure you don't check this directory into SVN, either mark it "Derived" via Properties or add it to SVN:ignore via Team->Add to SVN:ignore.
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