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I have a web project and use Tomcat for my development. IDE updates nbproject/project.properties file according to this settings. Now another developer joins the same project but decides to use Glassfish as a target server and this file is regenerated. And because this file is versioned we are in a state where we can rewrite our changes repeatedly or waste our time watching for what should be included in a commit and what not. Same for ant-deploy.xml file.
Reassigning to Web Projects.
Current design assumes that same family of servers would be used for a project - server type is stored in sharable project.properties and concrete instance of the server used by user is in private.properties. Which does not hold for your usecase. I thought there might be a workaround in moving server type property (j2ee.server.type) from project.properties to private.properties. But that does not work - server type is always updated in project.properties. This is a valid issue - perhaps server type property update should be smarter and either keep it in private.properties if that's what used did by hand or do not update it in case of valid server instance property. The later case is there likely for a reason though and I wonder what would got broken if I changed that.
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