Your best bet would be the following:
1. Configure your project for third-party version control
and push it
to the remote repository.
2. Add the plugin in the Plugins folder in the remote repository. Make sure that the folder structure of Plugins becomes something like this:
other files and folders
your modified project in AppBuilder.
If you don't want to go this way, I suggest extracting the plugin archive locally and adding its files in batches following any of the approaches described here
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