fix process java resource issue

[xckevin]

暂时修复atlas不能处理主工程的java resources的问题。目前来看atlas设计思想仅对主工程so做了限制，所以在这里判断是merge resource直接调用super的方法处理；如果未来需要对主工程java resource做管控，需要将type传到 AtlasIncrementalFileMergeTransformUtils#toNonIncrementalInput 做进一步判断

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