We work with the composer differently. With a composer, our application only cares about its code. In fact, if you are kork using git, you have to add the yii folder to .gitignore couse - this is not your application folder. This is the symfony path.
What about Yii !? First of all, I suggest you start yii projects with:
$ composer create-project yiisoft/yii path/to/your/project
This is the way Yii works with yii and the composer. After that, when you complete the yii download, the composer asks you if you want to store the yii git files or not. You can simply say no and manually delete these files manually. You can also try fork yiisoft / yii and improve this behavior so that this file deletion happens automatically.
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