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If some files are changed by a another program, Netbeans doesn't find these changes before commiting the files to the repository. The command line client and other svn clients check every file in the tree to be commited for modifications before commiting, but Netbeans does not. Please change this annoing behavoir.
When making external changes you should always run 'refresh status' from the versioning view. You may also try running netbeans with switch -J- Dnetbeans.subversion.commit.deepStatusRefresh=true. *** This issue has been marked as a duplicate of 118832 ***