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The only Vim or Neovim plugin I have found that can handle git operations on symlinked files is the sadly deprecated gina.vim. Neither vim-fugitive nor neogit work in my testing. If anyone knows of a maintained plugin that can commit changes to a symlinked file, please let me know in the replies.
Straight from the vim-fugitive README, but did you try fugitive with https://github.com/aymericbeaumet/vim-symlink ?
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