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Because Atom was created by Github I persume.

So they should ship it as a promotional tool?

You can make the argument that they want to encourage you to submit patches to the project which is on github.

It's kinda the same deal with GNU Emacs which bundles a whole bunch of stuff that is directly related to the GNU project.

Really at the end of the day it's a fork away to shipping with SVN,CVS,mercurial,gitlab or whatever.

Disable it if you don't like it.

Many of these features already exist as an optional package.

Lots of people use GitHub anyway