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this is related to the issue 87811 but for version 5.5 of netbeans. I was not able to run the zip distribution. On examining the shell script generated in the bin directory I think I found the problem. Changing the line clusters=`cat "$progdir/../etc/$APPNAME".clusters | readClusters` to clusters="$progdir/../myapp:$progdir/../harness:$progdir/../ide7" seems to work. So it looks like the readClusters function is not working. I am not an expert in shell scripting and not exactly sure how to fix this though.
just to add the readClusters function did this to clusters variable -n -n ./../myapp -n : -n ./../harness -n : -n ./../ide7
i've done some fixes in this changeset for 6.1-M2 http://hg.netbeans.org/main/rev/472f58316333 apart from that, the XXX.App application folder was created for me correctly, so I suppose it was fixed. If you get the same problem in upcoming 6.1-M2 (or beta), please reopen with steps to reproduce