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Reproduce: create a PDE launch configuration with "Use features in the workspace" mode enabled. The tree with plugins is disabled. Close the configuration dialog and open it again. You will see that the tree with plugins is not disable while it's supposed to.
Reproducable on Gentoo Linux, GTK. Will provide a patch in the next hours.
Created attachment 54022 [details] plugintree.diff Attaches is a patch which should fix the bug. Patch is against current HEAD.
Benjamin, thanks for the patch. I am releasing it with a minor modification. Instead of explicitly calling PluginBlock.enableViewer() after calling PluginBlock.initializedFrom(..), I added an extra boolean parameter to the PluginBlock.initializeFrom function for the value of fUseListRadio.getSelection(). I did this so we don't call enableViewer twice when initializing. This should help performance and prevent any flickering on slower machines. Should be in 3.3M4.