I guess that when users make the habit of using the free tool, then the company that provides it can easily embed other convenience habits that could potentially lead to a future sale.

Both Microsoft and Github have commercial products to sell at a later stage, VSCode has now integrations with Azure, I don't know about Github integrations on Atom but the potential is there.

When the user is using your free tool you are one step closer to provide something additional that is so convenient that is hard to say no, even if is paid.