"me too". Firefox tries to open zip files in gedit. In Nautilus they are
correctly associated to file-roller.

Removing this line seemed to fix the issue:
application/octet-stream=gedit.desktop;inkscape.desktop;

I believe the bug is NOT in Firefox, but in whatever adds the line to
the mimeapps.list. It should be in sync with the file associations used
by Nautilus. I don't know enough details of this mechanism to suggest
the correct fix.

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https://bugs.launchpad.net/bugs/918019

Title:
  Firefox does not use default application to open binary files

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