Some file missing after rebuild in version 5.0,why?

I put a file named Log4j.properties in the directory
("/WEB-INF/classes" ) in my project, my java files and class files is also put in the directory or its subdirectory , i found that if i rebuild the project
once or twice , the file will be cleaned .
It never happens in version 4.X , can somebody help me ?

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I find that the files that defined in "settings -compiler - resource patterns" will be cleaned in
rebuild .

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