I'm using Ubuntu 16.04 and latest Eclipse Neon. When I hover some code, I got my tooltip background black and my text orange. I found it here I must change colors at OS level. Here I saw how to edit colors at OS level. However it didn't work. Even changing Ubuntu Theme, changing tooltip color on Eclipse. I'm using Ambiance right now.
2 Answers
(Duplicate of https://stackoverflow.com/posts/40360725/)
I have verified that
export SWT_GTK3=0
is a viable, albeit suboptimal, workaround in Ubuntu 16.10 and Eclipse 4.6.1 when the desktop appearance uses the BlueMenta themes, with no additional tweaks required.
Tweaking the gtk-3.0 css files didn't work for me.
Other users have had better luck with the scripts in this project

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Very late answer, but after some annoying trials (mostly for older Eclipses with GTK2) a simple solution for brand new eclipse 2019-06 and perhaps for other eclipse versions using GTK3:
Install the color-themes-plugin via
Help>Install New Software
use the plugin via
Window>Preferences>General>Appearance>Color Theme
choose any other then default-color-theme, apply and close Dialog
If you still want to use Default-Theme: reopen Dialog and switch back to default

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