PlugClean required for manually cloned plugins

I usually backup my whole .vim/ and .vimrc to github and pull them to new machines. You can find my repository [here](https://github.com/archerindigo/vimrc). Those 3rd-party plugins I use are set as git sub-modules so they would be cloned from remote along with my repository. However, when I try to update the plugins using PlugUpdate, "PlugClean required" will prompt so I have to clean all my plugins and install them again.

How can I avoid this situation? Is there some point that vim-plug record the status of the plugins such that this error occurs even though the plugins are at the same commit when I backup?


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- Type:
- [ ] Bug
- [ ] Enhancement
- [ ] Feature Request
- [x] Question
- OS:
- [ ] All/Other
- [x] Linux
- [ ] OS X
- [ ] Windows
- Vim:
- [x] Terminal Vim
- [ ] GVim
- [ ] Neovim