if you use :GFiles instead of :Files it will ignore everything that is in .gitignore. That should solve the cases you mentioned, although it does not provide a general answer.
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How do you go by ignoring directories such as
node_modulesor.githubif you use
:GFilesinstead of:Filesit will ignore everything that is in.gitignore. That should solve the cases you mentioned, although it does not provide a general answer.