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I have no idea what happened. All of a sudden applications on elementary started having white gaps and misplaced content. This happened after I tried to install GNOME Builder. Can some one help me out without needing to reinstall Elementary? Here are some images:

screenshot 1 screenshot 2

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Just looking at the screenshot, my best guess is that you've unknowingly upgraded your system to a newer version of Gtk+ that is incompatible with the elementary stylesheet. This makes Builder work, but it might cause issues with other apps.

To check which version of Gtk+ you have installed, you can run the Terminal command:

sudo apt-cache policy libgtk-3-0

You should see some output like:

libgtk-3-0:
  Installed: 3.18.9-1ubuntu3.1
  Candidate: 3.18.9-1ubuntu3.1
  Version table:
 *** 3.18.9-1ubuntu3.1 500
        500 http://us.archive.ubuntu.com/ubuntu xenial-updates/main amd64 Packages
        100 /var/lib/dpkg/status
     3.18.9-1ubuntu3 500
        500 http://us.archive.ubuntu.com/ubuntu xenial/main amd64 Packages

This tells me that I have version 3.18.9 installed. This is the original version that ships with elementary OS.

If you have a newer version of Gtk+ (like 3.20), you can either try to manually edit the stylesheet to fix issues yourself, switch to a stylesheet that supports whatever version of Gtk+ you've upgraded to, or try downgrading Gtk+ to the original version shipped with elementary OS.

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