It's not clear what the bug is/was. I can no longer reproduce with
Eclipse Kepler in Ubuntu 14.04.

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https://bugs.launchpad.net/bugs/1066569

Title:
  Eclipse Freezes, Causes Hard System Freeze

Status in “eclipse” package in Ubuntu:
  Confirmed

Bug description:
  During routine use on Ubuntu 12.04 64-bit, Eclipse Indigo (version in
  repos) intermittently will freeze and become unresponsive (Window is
  grayed-out, CPU maxed out). Occasionally this causes the entire system
  to freeze (no input accepted, images on screen frozen). The only way
  to recover from this freeze is to hold the power button down for a
  hard reset.

  The problem is intermittent- repeating the same sequence of actions
  which led to a freeze cannot produce another freeze.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: eclipse 3.7.2-1
  ProcVersionSignature: Ubuntu 3.2.0-32.51-generic 3.2.30
  Uname: Linux 3.2.0-32-generic x86_64
  ApportVersion: 2.0.1-0ubuntu13
  Architecture: amd64
  Date: Sun Oct 14 14:21:51 2012
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release amd64 
(20120425)
  PackageArchitecture: all
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: eclipse
  UpgradeStatus: No upgrade log present (probably fresh install)
  modified.conffile..etc.eclipse.ini: [modified]
  mtime.conffile..etc.eclipse.ini: 2012-10-03T19:20:58.144219

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