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The box to the right of the 'select a project' tree view does not do anything and is a relic from the JavaDoc wizard where it can be used to refine selections to individual classes. The box should be removed in the AJDoc wizard.
Now fixed - changed the wizard to use a CheckboxTreeViewer, which only has one pane instead of a CheckboxTreeAndListViewer which had two. AJDT 1.2.1: BUILD COMPLETE - build.540 Date of build: 10/04/2005 15:38:42 Time to build: 45 minutes 41 seconds AJDT 1.3.0: BUILD COMPLETE - build.135 Date of build: 10/03/2005 16:08:48 Time to build: 32 minutes 37 seconds