Good. Some time ago, since it was open, but it is not, you can have a git nested structure in some repository that I worked on in the git folder, like in every plugin folder. However, subfolders are ignored by the gitignore file. This is another problem. My solution was to delete the .git folder and start over as it was a new project, in my case I renamed the directory and the project since I had a typo in the name.
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