For long-lived forks when the goal isn't to merge back upstream - I prefer using .diff files + a some scripts to apply them.

I couldn't find a tool that was close to my adhoc scripts. So I built Patchy to help manage my patch sets:

You clone the repo you're "forking" locally, make changes directly, then run:

  patchy generate   # saves changes to ./patches as .diff files

Later you can reapply your patches programmatically with:

  patchy apply

There's also helper commands to clone extra copies of the repo, reset them, etc.