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It should be possible to configure Netbeans to use an external diff/merge tool.
It is already possible to use an external diff: Tools -> Options -> IDE Configuration -> Server and Extrenal Tools Settings -> Diff and Merge Types -> Diff Engines -> Command-line Diff. You can specify the diff command, where {0} and {1} is replaced with the files to compare. The merge can be considered for the future...
The 'engine-toolbox' which lets you choose the command-line-diff is only available if you diff by using Tools->Diff. It is unfortunately not available if you choose CVS->Diff_Graphical. (But that's another issue). Back to this issue: That possibilty only works well for 'real' diff commandline tools. That means that the tool has to return output (in proper format) which is then used by the graphical component of netbeans. But I was looking for a possibility to use a completley external diff/merge application which its own graphical component (such es KDiff3, e.g). Such programs are not going to function very well in that way: Netbeans is always waiting (not responding) until the external app is closed and after that netbeans complains about bad data (no data) recieved from that application. That's what this enhance request was ment for.
Good analysis - Incidentally , if you is searching for a service to merge two PDF files , my husband encountered a service here http://www.AltoMerge.com/ and also here http://pdf.ac/7xW6tQ