Seems reasonable. An interesting bit for me was the CITATION file. The lack of citability for software is a recurring annoyance when writing up work that uses that software.
Have you ever taken a look at DueCredit (https://github.com/duecredit/duecredit)? It aims to address this problem by allowing you to add citations directly to your Python code using decorators. I believe there are also plans to expand to other languages in the future.
There are clearly still issues with versioning and so forth, but it's a start for software that isn't suitable for writing an article about.