Eclipse does have per-user configuration, at
$HOME/.eclipse/org.eclipse.platform_$version_$id/configuration/ ;
however, I don't know if that particular setting can be changed there.

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https://bugs.launchpad.net/bugs/485167

Title:
  There should be a eclipse.ini file in user's home directory

Status in “eclipse” package in Ubuntu:
  Triaged

Bug description:
  Binary package hint: eclipse

  Hi:

  I noticed that eclipse uses the configuration file
  /usr/lib/eclipse/eclipse.ini, which contains amongst other settings,
  the maximum amount of heap space for the JVM.  It seems to me that
  such a setting will increasingly be modified by end-users, and thus
  should be configurable from a file such as ~/.eclipse/eclipse.ini
  (i.e., in the user's home directory).  This would make it behave the
  same way as most linux programs out there.  Is there some reason that
  this isn't done?

  Reading the bug report at
  https://bugs.launchpad.net/ubuntu/+source/eclipse/+bug/43162, comment
  #5
  (https://bugs.launchpad.net/ubuntu/+source/eclipse/+bug/43162/comments/5)
  states that they've very recently (a few days ago) moved the
  eclipse.ini to be in /etc.  Again, this doesn't seem to fit the common
  model of having configuration be overrideable by a file in the user's
  home directory.

  Cheers

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