In the retro console scene, sadly there are many programs with multiple independent forks which cannot be merged together.
Famitracker is a NES composing program. It was originally a monolithic cathedral project written by jsr without a Git repo. There were several forks made, including HertzDevil's 0CC-Famitracker which had a Github repo and added features. Famitracker's creator released a "beta" without source code, then abandoned the project. 0CC-Famitracker reverse-engineered the binary to merge in some features. I maintained a "bugfix patch-set" on top of 0CC for several months, but kept running into merge conflicts, so I ended up forking an older revision of 0CC, calling it j0CC, because 0CC's maintainer was adding bugs and refused to accept contributions (including bug fixes). Then we both abandoned our forks...
libgme is a library which emulates game-console sound chips, and is used in media players. It was originally written by blargg, but now has 2 active forks: A "linux" fork packaged in many Linux distros (including Ubuntu/Fedora), currently lightly-maintained by mpyne (which suffered a security vulnerability), and a "windows" fork used with foobar2000 (also builds on Linux via qmake) maintained by kode54, which is more ambitious with changes, including a slow but accurate SNES SPC700 emulator written by byuu and not affected by the security vulnerabilities.
I heard Amiga emulation (UAE) has multiple forks too, and WinUAE is more popular?
I would prefer if the forks had never happened, but it's not going to happen.