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Currently the sources displayed by the debugger in the Sources window are only those obtained from GlobalPathRegistry. It would be better to also display in the Sources window sources learned in other ways (e.g., from the run classpath through SourceForBinaryQuery, or from the <sourcepath> property of the <nbjpdaconnect> task), even if these sources are not registered in GlobalPathRegistry. The debugger currently uses these sources, but it just doesn't display them in the Sources window.
I agree that this should be displayed. See also associated issue #51761.
Changing TM for open issues.
In 6.5 when debugging a project, the source-path is taken from conversion of it's class-path. Please verify.
Verified ... and Closing all issues resolved into NetBeans 6.7 and earlier.