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And I don't know anything about stow as I just use my own simple install script
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You can try chezmoi dotfile manager. It uses .chezmoiexternal.toml to download files to home directory.
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InfluxDB
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It's ideal for dotfiles. Here are mine
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I'm not sure about vim-plug, but I use minpac which does use vim's native plugin location. The selling point is that the installs and updates are managed via the plugin's commands. As part of my dotfiles, the install command is run.
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I'm perfectly happy with ~/.vim in a separate git repository (mine), with all the plugins installed via vim-plug.
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Regarding the size, I don't think I have this problem as well. I just cloned my dotfiles and run du -h -d1 . there:
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WorkOS
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[".vim/pack/vendor/start/nerdtree"] type = "git-repo" url = "https://github.com/preservim/nerdtree.git" refreshPeriod = "1s"
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git --git-dir=$HOME/.home.git --work-tree=$HOME submodule add add https://github.com/tpope/vim-commentary.git ~/.vim/pack/plugins/opt/vim-commentary
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