This is quite a disappointment, i love this IDE so far. Some great features, loving the test runner. I have read all the docs on setting up GitHub and have the Changes tab work great.
But yes, the lack /src is a challenge to sharing what i am working on in a GitHub repo most of the SF community is used to seeing, that being one with a /src in the root. Sadly lack of a /src folder also breaks my GitHub Salesforce Deploy button as well. I can also see this being a challenge for enterprise devs, where IDE choice is flexible and as such consistency with the use of /src is vital.
I like Jeff’s solution, but as has been pointed out kinda erodes all the things i love about this IDE so far. I’m starting to wonder if there is a solution involving some use of symbolic folder links and git ignores perhaps?