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NetBeans 6.1 installed from installer have weird permissions in some directories. For example the files in directory /Applications/NetBeans/NetBeans 6.1.app/Contents/Resources/NetBeans/nb6.1/modules there are .jar files which have -rw-r--r-- while the permissions of the folder are rwxrwxr-x. So that the permissions of .jar files should be -rw-rw-r-- This issue causes that it is not possible to rewrite .jar files by NetBeans itself.
In fact, permissions are lost during pack200<->unpack200 cycles. The fix would be pushed to main as soon as SPB site would be back online..
Fixed in main. http://hg.netbeans.org/main/rev/429b709cadda
Integrated into 'main-golden', available in NB_Trunk_Production #296 build Changeset: http://hg.netbeans.org/main/rev/429b709cadda User: Dmitry Lipin <dlipin@netbeans.org> Log: Issue #138095 Weird permissions of .jar files
Verified in build #200807240010.