I have just opened a bug against gedit in the Gnome project bugzilla:

https://bugzilla.gnome.org/show_bug.cgi?id=689621

The patch proposed by "Sabina Jung" is attached there as well.

** Bug watch added: GNOME Bug Tracker #689621
   https://bugzilla.gnome.org/show_bug.cgi?id=689621

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https://bugs.launchpad.net/bugs/995747

Title:
  Gedit: Remove trailing spaces feature removes last line.

Status in set of plugins for gedit:
  New
Status in “gedit-plugins” package in Ubuntu:
  Confirmed

Bug description:
  Ubuntu 12.04 LTS, 64Bit
  Gedit 3.4.1

  Here's what happend.
  1. Launch gedit.
  2. Create new file type. I am writing PHP file when I noticed it. So I 
created a PHP file.
  3. Put some codes/strings in there. Be sure your last line is a text.
  4. Use Remove trailing spaces feature of gedit.
  5. Observe, the last line will be trimmed.

  
  I expect, only trailing spaces will be removed.
  I found out that the last line was also remove.
  I also use other programming languages and still removes the string.
  Attached is the sample string I made.
  Open it with gedit 3.4.1 and remove trailing spaces.
  The comment should not be removed.

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