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If the build script works with source roots outside the project directory, or creates build products outside it, autoproject should remember this and register itself as an external owner. (Less important than for freeform projects since normally external roots are used to avoid putting NB metadata into a project directory, not an issue for autoprojects.)
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