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I want to ignore only two files in my SVN, I am using Netbeans. These both are the config.php files located at different locations in same project.

+1  A: 

In your working copy, go to the parent directory of both of these config.php files, and set the svn:ignore property on those directories to config.php.

cd dir1 # assuming dir1/config.php is one of the files to ignore
svn propset svn:ignore config.php .
# repeat for dir2

Don't forget to commit!

Michael Hackner