I'm using the version of herbstluftwm which is found Ubuntu 14.04 repo.
Then I downloaded the latest version of eclipse from their website and tried to run it but it didn't run well. Here is a screenshot of it:
http://imgur.com/QmmubV8
The space between below the grey window cannot be removed. It is as if there is an invisible window that is taking this place
I switch to Unity and run the eclipse from there and there weren't any problem.
I also installed eclipse from the repo and it worked in herb window.
It might be worth mentioning that I'm using dark theme of eclipse. Here is a screenshot of the theme:
http://imgur.com/cwFTeZb
The source of the theme:
https://github.com/guari/eclipse-ui-theme