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If you convert some filesystem to webmodule or create new webmodule and than you want to exit IDE, you will be informed that file "context" is not save. After deployment context is saved.
problem is in j2eeserver
Checking in src/org/netbeans/modules/j2ee/deployment/config/ConfigSupportImpl.java; /cvs/j2eeserver/src/org/netbeans/modules/j2ee/deployment/config/ConfigSupportImpl.java,v <-- ConfigSupportImpl.java new revision: 1.6; previous revision: 1.5
*** Issue 39109 has been marked as a duplicate of this issue. ***
verified