My take on this is that you should treat Lyra as a “total conversion,” or as a “copy and paste re-use.”
If you already have a game, you copy-and-paste the bits that you want out of this project, to merge into your game.
If you’re starting a new game, rename this one from Lyra to YourGame, and start editing inside the actual code/assets of the sample. The code does not look like it’s set up to receive easy API-preserving updates from upstream changes, so any “later update” would have to be big surgery anyway.
If there is a later version with bug fixes you want to include, the best way to do it, is likely to do a three-way merge with the original Lyra as the base. See what changed from Lyra-Base-Old to Lyra-Base-New, and fold those changes into your code if it’s easy, or make a note to make those same changes in your code, if it’s a hard clash.