Branches + Source Control Git helps a ton. but even an older source control system like SVN would be better than nothing. http://rogerdudler.github.io/git-guide/

@alexpul What I do a) I do not change boot.py a lot. I have only command related to the general operating mode in there, like USB REPL enabled or WiFi access, although the latter may vary b) I do not code for specific things in main.py. Instead if put that into files with appropriate names and import them in main.py. If one application consists of several files, I put them in a subdirectory and either uos.chdir() into that, or alin sys.path to include that subdirectory, such that import can find the files.