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The way to endorse libraries for a java command is to use the -Djava.endorsed.dirs= switch at the command line. Setting it up in an IDE is slightly different. In Eclipse I add them to list of system libraries in the JRE definition (Help\Preferences\Java\Installed JREs\Edit the one you want to add them to, move them to the top of the list), and add a -Djava.endorsed.dirs=<Path to the endorsed libs> argument into the Default VM Arguments box for good measure (the latter does seem to be necessary, and makes it obvious to me that I'm modified this JRE)
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