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Build from 11/26, JDK 1.4 Create a web module. Do a change in index.jsp and save it. It's saved immediately. Now add to the project a Web Service or Web Service Client. After it is finished go to the index.jsp and try to save any change. It takes much longer than before. All files under Web Pages are influented, not only jps files. It can be connected with issue #69131 , but I'm not sure.
Marku, profile it, please.
Based on an offline discussion with Petr I am closing as worksforme. (The problem was caused by some local changes done on Petr's repository).