Why Idea 13.1.3 is copying all files again for any jar change

We have pretty huge project containing over 10K classes and enourmous number of files(jsp and asset files), If I change any jar in idea(add new one, delete existing one) then start the tomcat Idea starts copying all compiled files from production to artifacts, .jsp files also be copied from project itself to artifacts. It takes forever to finish copying. My question is why idea is copying over again, It does not recompile all jave files which is correct, But WHY it is copying the files from production folder that are not changed or compiled newly? This was never issue since version 6. This started happening in new version of 13.1.3. It happened on mac and windows.
I asked this question 3 month ago, None answered, I am quite devastated due to the behavior of idea now, since I change jars daily for my tasks and have to wait quite long time for single change. Any idea what is wrong?

Thanks.

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Anyone can help?
yes? no?

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