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I have a number of web projects open in 6,7 rc1 (problem existed in earlier releases of 6.7 as well, have not verified if it is present in 6.5 but I would imagine so). These projects are all "webproject with existing source" and tomcat 6 projects. I do not deploy or run them through NB, all is done through a series of ant tasks. However whenever I run an ant task externally to NB I get a box up in NB saying "Deployment descriptor directory can not be found. It may have been removed or renamed." This box should contain more information, at the very minimum it should contain a reference to which project it refers to. Best possible would be if it would also say "To fix this problem a directory needs to be created in /path/to/missing/directory" Turing off "deploy on save" seems to remove the message, but the problem still remains that the message is not informative enough to enable a user to take appropriate action.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss