Fixes #539.
Was already merged in Bitbucket before import, marked as merged by the import user
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Sort entries in ui.commands in alphabetical order.
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Sort entries in ui.handlers in alphabetical order.
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Fixed deprecation notice on ViewerSorter.
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Fixed deprecation notice on IDE.getEditorDescriptor.
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Fixed deprecation notice on Plugin.savePluginPreferences().
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Fixed deprecation notice on ContextChangeSet.getComment() in the Mylyn API.
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Fixed some warnings about using deprecated methods.
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Code cleaning: made some methods static.
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Removed implementation of an org.eclipse.core.resources v3.12 method after setting the API baseline to Neon.R (v3.11).