Not an actual answer, more additional info that I hope will help track down the problem. I am having the same issue with Version: 2018-12 (4.10.0), Build: 20181214-0600.
I opened the workbench.xmi file mentioned above. This was the section I found by searching for "Open a Terminal", which is the tooltip on a repeated icon.
<children xsi:type="menu:ToolBar" xmi:id="_tODFlzriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.toolbar">
<tags>Draggable</tags>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFmDriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFmTriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFmjriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFmzriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFnDriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFnTriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFnjriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_tODFnzriEem5AdcasuU54g" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_tOOFADriEem5AdcasuU54g">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
</children>
- Stopped eclipse.
- Edited this down to one menu:HandledToolItem child.
- Started eclipse.
When I refreshed workbench.xmi I found this (two icons appear):
<children xsi:type="menu:ToolBar" xmi:id="_FzpBgzrrEemLeYohrjtX4w" elementId="org.eclipse.tm.terminal.view.ui.toolbar">
<tags>Draggable</tags>
<children xsi:type="menu:HandledToolItem" xmi:id="_FzpBhDrrEemLeYohrjtX4w" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_Fzw9IzrrEemLeYohrjtX4w">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
<children xsi:type="menu:HandledToolItem" xmi:id="_FzpBhTrrEemLeYohrjtX4w" elementId="org.eclipse.tm.terminal.view.ui.commands.launchToolbar"
iconURI="platform:/plugin/org.eclipse.tm.terminal.view.ui/icons/eview16/console_view.png" tooltip="Open a Terminal" command="_Fzw9IzrrEemLeYohrjtX4w">
<persistedState key="IIdentifier" value="org.eclipse.tm.terminal.view.ui/org.eclipse.tm.terminal.view.ui.commands.launchToolbar"/>
</children>
</children>
I notice, also, that the ids have been updated.
John