I get Eclipse 3.8 in apt-get, and having a problem with .nb files with it here about How to Have Mathematica 10 Workbench in Ubuntu 16.04? I do not understand how this can possible that only 3.8 in apt-get, since 3.8 is already two years old.
Configure Java PATHs for Eclipse. So install JRE >=7 and Java PATHs correctly in your system for Workbench 3
> Configuring your Java Run-time Environment (JRE) or Wolfram Engine installation are still both necessary on Linux. Further, the version of JRE used should be at least version 1.7
The .nb problem is caused by false setting of Java path in your system/Mathematica.
You can't get it directly from the standard Ubuntu repository, but you can add this PPA that has Eclipse 4.5 through apt:
sudo apt-add-repository ppa:mmk2410/eclipse-ide-java
Ref: https://launchpad.net/~mmk2410/+archive/ubuntu/eclipse-ide-java
The best way is using umake Ubuntu Make is a project designed to enable quick and easy setup of common needs for developers on Ubuntu.
And that's it
To use third party ppa's is always a risk and cannot be used in all environments. Do to get rid of apt-get's eclipse which is old
Get and extract the official tarball in Eclipse homepage and do
Configure Java PATHs for Eclipse. So install JRE >=7 and Java PATHs correctly in your system for Workbench 3
The .nb problem is caused by false setting of Java path in your system/Mathematica.