Some years ago, it was announced that Microsoft had done a deal with Donald Knuth and the American Mathematical Society and had bought the rights to TeX. It was slightly worrying until you noticed that the announcement was dated 1 April.
Now I see that the company which has fought a long and bitter war against open source software is to buy GitHub, according to the BBC news. And April is long past.
When Microsoft bought Skype, I found it would no longer run on my Linux laptop. So should we be worried that they have bought GitHub? I don’t use it myself, but a lot of the excellent free software that I do use, such as GAP, is now developed there. Are they buying it to destroy the competition, as the railways did to the canal network in Britain in the nineteenth century?
I have great admiration for the boss of Microsoft, but nothing but fear and loathing for his company.
Peter Cameron's Blog 
I think there is not so much to worry about.
1. Skype works perfectly fine with Linux. I use it all the time on an Ubuntu installation.
2. Microsoft has essentially shifted its focus to work to include open software, and largely given up its hostility to external developers. See, specifically, https://medium.com/@ow/microsoft-acquiring-github-is-a-good-thing-heres-why-6a6a57eb83ac
3. There is no reason to believe, before or now, that GitHub will exist forever. But is just a repository: a virtual, mirrored file system. It is not a big deal to shift to a different host.
All the best,
Maybe so, but: re 1, not on mine (though I don’t care enough to try to sort it out); and re 2, the words “leopard” and “spots” come to mind.
Skype for Linux got an update fairly recently after years of being ignored by Microsoft. The old version had a lot of problems (indeed, it eventually stopped working entirely on my machine as well) which seem to have gone away with the new, so it’s possible that it would work now.
It is better to compare GitHub to an online platform to collaborate on TeX, such as sharelatex or cocalc.
(and git to TeX).
In GitHub’s case collaboration is on git repositories.
Later they also website hosting (with content held in a git repository).
there are alternatives to GitHub: GitLab, bitbucket.org, Trac, etc…
I have had concerns that Microsoft has been spoiling to take over Linux to destroy the competition. Hopefully, that won’t be possible. Microsoft desperately needs a serious competitor, and so far, it has had a near-monopoly that is really rather disgusting. Hopefully Microsoft’s acquisition of GitHub won’t negatively impact the Linux community.