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If I commit files in NetBeans to subversion, it will often leave out files that are several directories deep, if those directories are not clicked open in the projects pane (or favorites, whichever applies). This is a big headache as you can imagine because you can think you have committed a file and it didn't really commit. I have noticed this problem as early as Netbeans 6.5. I am on Windows XP currently using 6.7.1.
Try workarounds mentioned in issue 164277 *** This issue has been marked as a duplicate of 164277 ***