Unity 5.5 keeps thinking it's a beta so it redoes everything (yet another bug)

Well along that same line of thinking I suppose that nominates you for the laziest person ever.

Try deleting ProjectVersion.txt in the /ProjectSettings/ folder. You can also try deleting the entire /Library/ folder.

Yeah, unfortunately we included a library folder with the example project from the beta, so for now just delete the library folder like mentioned above ^.

Welp, that went south quickly.