Hiding Duplicate Toolbars Items in Eclipse

I've been having the same problem since upgrading to Oxygen. I haven't been able to reliably reproduce the issue.

The workaround suggested by @howlger has helped and is less intrusive than blowing away the entire workspace:

1. Close Eclipse.
2. In the Eclipse workspace directory, delete the .metadata\.plugins\org.eclipse.e4.workbench\workbench.xmi file or just rename it so you can bring it back in case you need to revert.
3. Open Eclipse.
4. Rearrange the UI elements to your liking.

This is a pain, but does remove the duplicate elements from toolbars.

I also found that customizing the perspective doesn't work for duplicated items, but does for non-duplicated:

1. Window -> Perspective -> Customize Perspective...
2. On the "Tool Bar Visibility" tab, deselect the items that are cluttering up your toolbar.

This appears to be an issue in the core Eclipse platform. While the screenshot shows pretty icons thanks to Darkest Dark, it does not appear related at this time to Darkest Dark plugin as Howlger has indicated. Instead, it appears that duplicate contribution entries appear in the workbench.xmi file. In our testing (I contribute to Darkest Dark), we can see these entries happening in a standalone Eclipse, though haven't been able to track down the root cause yet in where entries get added again to the workbench.xmi.

Interestingly, a user has posted on an old Eclipse bug with what looks like a screenshot of Eclipse Classic exhibiting the same problem today.

https://bugs.eclipse.org/bugs/show_bug.cgi?id=402561

Screenshot from Eclipse Bug

It looks like you have installed the Darkest Dark Theme plug-in. Try to uninstall it.

This closed source plug-in does load-time weaving to patch Java bytecode of the Eclipse platform (for legal reasons, to not have to publish their changes). In contrast of using a public API, load-time weaving patches have to be adapted for each (new) Eclipse version: an error in the plug-in can cause strange behavior of the Eclipse platform.

See also: Keyboard shortcuts in Eclipse Oxygen stopped working