The .Project files are Codesys 3 like it says on the page. You can download it for free and run simulations, the runtimes are what costs money.
As for mark down aka .md files they are just the standard way you make readmes on GitHub.
Side note: Codesys is leaps and bounds the best and most powerful PLC programming environment I have ever used. If you ever have choice on PLC vendor for a project always go with a manufacturer that uses Codesys. Wago and Modicon are a few examples.