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build.properties should have a comment saying that it is a generated file and that changes will be overwritten. This would help users who seek to understand where netbeans actually stores its information and which config file can/cannot be edited manually. (I expected that build.properties could be edited just like the *.properties files in nbproject.)
Actually I believe only the properties corresponding to library definitions will be overridden but that other properties will be left alone - Tomas can you confirm or deny? Anyway, I agree this would be the right thing to do.
Yes, the libraries properties are overriden when the library definition changes, also the default.javac.source and default.javac.target properties are changed when you change the version of JDK the IDE is running on. The platform properties are kept synchronized with platform definitions in the same way as libraries, if you change the definition the properties corresponding to the platform are changed. If you add some other properties to this file, they should not be changed by the IDE, it is save to add properties but it is not save to modify the generated properties. The commen in the file is right thing to do, maybe it would be better to put such a comment to every generated property in this file.
The following properties are generated from other sources and are not safe to edit: default.javac.* libs.* platforms.* copyfiles.classpath wsclientuptodate.classpath nbplatform.default.harness.dir nbplatform.default.netbeans.dest.dir Of course there is no way for projects/libraries to have an accurate list of all such properties, since other modules add some of them.
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