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It would be nice if you could tell NetBeans that <logical directory> should put files in <directory>, so whenever you copy/create a file to/in the logical directory that file should end up in <directory>. For example, I tell NetBeans that the logical directory "Source Files" should place new files in the "src" directory. Creating new files in that logical directory should place the new file in the connected directory. Copying files to the logical directory should create the file in the connected directory and not just a link (related to Issue 170658).