You'll want to add compulsory_for_desktop tags to the metainfo files of these 
applications: 
https://www.freedesktop.org/software/appstream/docs/chap-DistroData.html#tag-distro-compulsory_for_desktop
That will prevent removal of them.

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https://bugs.launchpad.net/bugs/1551467

Title:
  GNOME Software uninstalls other critical applications in Ubuntu 16.04

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