I've also come across this problem! For me its a huge issue because it basically cripples the functionality of netbeans and subversion as we have hundreds/thousands of files in the symlinked directories - imagine clicking exclude from commit for that many files! I have figured out a semi-workaround which might help out! If you have the 'projects' window open, select all files/folders (everything but the symlinked ones) you want netbeans to consider for versioning and right click on the selected files and goto 'Subversion' -> 'Show Changes'. Now you'll get a listing of all modified files that aren't in the symlinked directories. Now if you click 'commit all' it will only commit the files that are listed in the subversion pane and you don't have to worry about clicking 'exclude from commit' on all those files! One other thing: If the symlinked folder is underneath a parent folder... Deselect the parent folder and manually select everything in the folder except for the symlinked directory (using ctrl+click and ctrl+shift+click). It's far from optimal but at least it works!! I'd really like to see netbeans deal with the symlinked directories properly at some point however. Hope that helps!