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When filtering for features or plug-ins in the Run Configurations Dialog / Eclipse Application unsetting the filter does not fully re-populate the list but merely show all selected features. See the enclosed image for clearification.
Created attachment 250027 [details] Screenshot with bug depiction
Reproduced. Once you clear the filter, you don't see unchecked items, even if you toggle the 'show slected items only' setting. This will most likely be a bug in our filtered tree implementation.
Fixed via http://git.eclipse.org/c/pde/eclipse.pde.ui.git/commit/?id=a97fcea38fe5bf6dbd8abe120f51a96ab3213230 However if you keep on giving filter/removing filters text in plugin and feature drop downs, then after sometimes ( 4-5 times change), the feature section's features are all deselected. That is a separate issue that happens independent of this problem or fix. I plan to open a new defect of that issue.
Version: Mars (4.5) Build id: I20150429-2000