I believe that Netbeans can decide which dependencies it should compile for your project (maybe it can highlight errors in the editor / navigator).
As for why he now does this every time you open a project, I don’t know. I suspect that previous versions did this automatically, and this change is intended for users with huge projects who might not want to wait, and instead let them choose which modules they want to destroy the stuffing.
It would be nice if the option turned off, though.
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