It's not clear to me why there are both a README and a README.md file. Perhaps the intention is to merge the two? Then this should be recorded somewhere (e.g. this issue ;-).
Or perhaps they are meant to stay in parallel, which is also fine. But then I'd point from README.md to README. And I'd consider renaming README to e.g. NOTES or INTERNALS or whatever (and perhaps also convert it to Markdown?)