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Changes in this version relative to http://doclava.googlecode.com/
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* Modified the Java stub generator code to write out annotations for
methods and fields as well, not just classes. This meant adding a
writeAnnotations call to writeMethod and to writeField
* Modified the writeAnnotations method to take a "isDeprecated"
parameter, which when set adds a @Deprecated annotation if one
doesn't already exist. This ensures that APIs only marked with a
@deprecated documentation comment will also be marked as
@Deprecated. Also strips out @Override annotations.
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